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authorAaron M. Ucko <ucko@debian.org>2009-03-16 20:49:28 +0000
committerAaron M. Ucko <ucko@debian.org>2009-03-16 20:49:28 +0000
commite8f3513c621e07a1d0890d3dab064a122ef9533e (patch)
treec73627d1c752e77b6ff61687abfafa17dcb8c7ca /desktop
parentba8e66ff7c7810a0d5f2dbf3814e3a92f14bf2fe (diff)
[svn-upgrade] Integrating new upstream version, ncbi-tools6 (6.1.20090301)
Diffstat (limited to 'desktop')
-rw-r--r--desktop/aacomp.c1
-rw-r--r--desktop/biosrc.c1369
-rw-r--r--desktop/dlgutil1.c16
-rw-r--r--desktop/dlgutil2.c33
-rw-r--r--desktop/dlogutil.h4
-rw-r--r--desktop/import.c120
-rw-r--r--desktop/import.h4
-rwxr-xr-xdesktop/macrodlg.c1434
-rwxr-xr-xdesktop/macrodlg.h5
-rw-r--r--desktop/salfiles.c4
-rw-r--r--desktop/salpanel.c5
11 files changed, 2598 insertions, 397 deletions
diff --git a/desktop/aacomp.c b/desktop/aacomp.c
index 59baeec0..2aace79d 100644
--- a/desktop/aacomp.c
+++ b/desktop/aacomp.c
@@ -198,3 +198,4 @@ extern FloatHiPtr AAComposition (SeqPortPtr spp,
fptr = AAC (spp, start, end, numval, window, scr, res);
return fptr;
}
+
diff --git a/desktop/biosrc.c b/desktop/biosrc.c
index 4c001278..e3850e3c 100644
--- a/desktop/biosrc.c
+++ b/desktop/biosrc.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 1/22/95
*
-* $Revision: 6.90 $
+* $Revision: 6.93 $
*
* File Description:
*
@@ -161,6 +161,843 @@ typedef struct genbioform {
LookupTaxonomyProc lookupTaxonomy;
} GenBioForm, PNTR GenBioFormPtr;
+#ifndef WIN16
+static CharPtr taxlistMemStrs [] = {
+ "15\n",
+ "Acanthamoeba castellanii\t\t1\t4\tINV\t5755\n",
+ "Acanthoscurria gomesiana\t\t1\t5\tINV\t115339\n",
+ "Acetabularia acetabulum\t\t6\t1\tPLN\t35845\n",
+ "Acipenser sinensis\tChinese sturgeon\t1\t2\tVRT\t61970\n",
+ "Acipenser transmontanus\twhite sturgeon\t1\t2\tVRT\t7904\n",
+ "Acorus americanus\t\t1\t1\tPLN\t263995\n",
+ "Acropora millepora\t\t1\t4\tINV\t45264\n",
+ "Acropora palmata\t\t1\t4\tINV\t6131\n",
+ "Acyrthosiphon pisum\tpea aphid\t1\t5\tINV\t7029\n",
+ "Adiantum capillus-veneris\t\t1\t1\tPLN\t13818\n",
+ "Aedes aegypti\tyellow fever mosquito\t1\t5\tINV\t7159\n",
+ "Aegilops speltoides\t\t1\t1\tPLN\t4573\n",
+ "Aegilops tauschii\t\t1\t1\tPLN\t37682\n",
+ "Agrostis capillaris\t\t1\t1\tPLN\t204232\n",
+ "Agrostis stolonifera\t\t1\t1\tPLN\t63632\n",
+ "Ajellomyces capsulatus\t\t1\t4\tPLN\t5037\n",
+ "Ajellomyces capsulatus NAm1\t\t1\t4\tPLN\t339724\n",
+ "Alexandrium tamarense\t\t1\t4\tPLN\t2926\n",
+ "Alligator mississippiensis\tAmerican alligator\t1\t2\tVRT\t8496\n",
+ "Allium cepa\tonion\t1\t1\tPLN\t4679\n",
+ "Allomyces macrogynus\t\t1\t4\tPLN\t28583\n",
+ "Alternaria brassicicola\t\t1\t4\tPLN\t29001\n",
+ "Amblyomma americanum\tlone star tick\t1\t5\tINV\t6943\n",
+ "Amblyomma variegatum\t\t1\t5\tINV\t34610\n",
+ "Amborella trichopoda\t\t1\t1\tPLN\t13333\n",
+ "Ambystoma mexicanum\taxolotl\t1\t2\tVRT\t8296\n",
+ "Ambystoma ordinarium\tPuerto Hondo stream salamander\t1\t2\tVRT\t288796\n",
+ "Ambystoma tigrinum tigrinum\tEastern tiger salamander\t1\t2\tVRT\t43116\n",
+ "Amoebidium parasiticum\t\t1\t4\tINV\t4881\n",
+ "Amorphotheca resinae\tcreosote fungus\t1\t4\tPLN\t5101\n",
+ "Amphidinium carterae\t\t1\t4\tPLN\t2961\n",
+ "Ananas comosus\tpineapple\t1\t1\tPLN\t4615\n",
+ "Anas platyrhynchos\t\t1\t2\tVRT\t8839\n",
+ "Ancylostoma caninum\tdog hookworm\t1\t5\tINV\t29170\n",
+ "Ancylostoma ceylanicum\t\t1\t5\tINV\t53326\n",
+ "Anolis carolinensis\tgreen anole\t1\t2\tVRT\t28377\n",
+ "Anolis sagrei\tbrown anole\t1\t2\tVRT\t38937\n",
+ "Anopheles albimanus\t\t1\t5\tINV\t7167\n",
+ "Anopheles funestus\tAfrican malaria mosquito\t1\t5\tINV\t62324\n",
+ "Anopheles gambiae\tAfrican malaria mosquito\t1\t5\tINV\t7165\n",
+ "Anopheles gambiae str. PEST\t\t1\t5\tINV\t180454\n",
+ "Antheraea mylitta\t\t1\t5\tINV\t34739\n",
+ "Antirrhinum majus\tsnapdragon\t1\t1\tPLN\t4151\n",
+ "Antonospora locustae\t\t1\t1\tINV\t278021\n",
+ "Antrodia cinnamomea\t\t1\t4\tPLN\t279009\n",
+ "Aphanomyces cochlioides\t\t1\t1\tPLN\t112091\n",
+ "Aphis gossypii\tcotton aphid\t1\t5\tINV\t80765\n",
+ "Apis mellifera\thoney bee\t1\t5\tINV\t7460\n",
+ "Aplysia californica\tCalifornia sea hare\t1\t5\tINV\t6500\n",
+ "Aquilegia formosa\t\t1\t1\tPLN\t223430\n",
+ "Arabidopsis lyrata subsp. petraea\t\t1\t1\tPLN\t59691\n",
+ "Arabidopsis thaliana\tthale cress\t1\t1\tPLN\t3702\n",
+ "Arachis batizocoi\t\t1\t1\tPLN\t108210\n",
+ "Arachis duranensis\t\t1\t1\tPLN\t130453\n",
+ "Arachis hypogaea\tpeanut\t1\t1\tPLN\t3818\n",
+ "Arachis stenosperma\t\t1\t1\tPLN\t217475\n",
+ "Argas monolakensis\t\t1\t5\tINV\t34602\n",
+ "Argopecten irradians\t\t1\t5\tINV\t31199\n",
+ "Ascaris suum\tpig roundworm\t1\t5\tINV\t6253\n",
+ "Ascosphaera apis USDA-ARSEF 7405\t\t1\t4\tPLN\t392613\n",
+ "Ashbya gossypii ATCC 10895\t\t1\t3\tPLN\t284811\n",
+ "Asparagus officinalis\tgarden asparagus\t1\t1\tPLN\t4686\n",
+ "Aspergillus clavatus NRRL 1\t\t1\t4\tPLN\t344612\n",
+ "Aspergillus flavus\t\t1\t4\tPLN\t5059\n",
+ "Aspergillus flavus NRRL3357\t\t1\t4\tPLN\t332952\n",
+ "Aspergillus fumigatus Af293\t\t1\t4\tPLN\t330879\n",
+ "Aspergillus nidulans FGSC A4\t\t1\t4\tPLN\t227321\n",
+ "Aspergillus niger\t\t1\t4\tPLN\t5061\n",
+ "Aspergillus niger CBS 513.88\t\t1\t4\tPLN\t425011\n",
+ "Aspergillus oryzae\t\t1\t4\tPLN\t5062\n",
+ "Aspergillus terreus NIH2624\t\t1\t4\tPLN\t341663\n",
+ "Astatotilapia burtoni\t\t1\t2\tVRT\t8153\n",
+ "Aureobasidium pullulans\t\t1\t4\tPLN\t5580\n",
+ "Avena sativa\toat\t1\t1\tPLN\t4498\n",
+ "Babesia bovis\t\t1\t4\tINV\t5865\n",
+ "Bacillus cereus\t\t11\t0\tBCT\t1396\n",
+ "Bacillus clausii\t\t11\t0\tBCT\t79880\n",
+ "Bacillus licheniformis\t\t11\t0\tBCT\t1402\n",
+ "Bacillus subtilis\t\t11\t0\tBCT\t1423\n",
+ "Bemisia tabaci\t\t1\t5\tINV\t7038\n",
+ "Beta vulgaris\t\t1\t1\tPLN\t161934\n",
+ "Betula pendula\tEuropean white birch\t1\t1\tPLN\t3505\n",
+ "Bicyclus anynana\tsquinting bush brown\t1\t5\tINV\t110368\n",
+ "Bigelowiella natans\t\t1\t1\tINV\t227086\n",
+ "Biomphalaria glabrata\t\t1\t5\tINV\t6526\n",
+ "Blastocladiella emersonii\t\t1\t4\tPLN\t4808\n",
+ "Blastocystis hominis\t\t1\t1\tPLN\t12968\n",
+ "Blumeria graminis f. sp. hordei\t\t1\t4\tPLN\t62688\n",
+ "Boechera stricta\t\t1\t1\tPLN\t72658\n",
+ "Bombyx mori\tdomestic silkworm\t1\t5\tINV\t7091\n",
+ "Borrelia burgdorferi\tLyme disease spirochete\t11\t0\tBCT\t139\n",
+ "Bos indicus\t\t1\t2\tMAM\t9915\n",
+ "Bos taurus\tcattle\t1\t2\tMAM\t9913\n",
+ "Botryotinia fuckeliana\t\t1\t4\tPLN\t40559\n",
+ "Botryotinia fuckeliana B05.10\t\t1\t4\tPLN\t332648\n",
+ "Brachionus plicatilis\t\t1\t5\tINV\t10195\n",
+ "Brachypodium distachyon\t\t1\t1\tPLN\t15368\n",
+ "Bradyrhizobium japonicum\t\t11\t0\tBCT\t375\n",
+ "Branchiostoma floridae\tFlorida lancelet\t1\t5\tINV\t7739\n",
+ "Brassica carinata\t\t1\t1\tPLN\t52824\n",
+ "Brassica napus\trape\t1\t1\tPLN\t3708\n",
+ "Brassica oleracea\t\t1\t1\tPLN\t3712\n",
+ "Brassica oleracea var. alboglabra\tChinese kale\t1\t1\tPLN\t3714\n",
+ "Brassica oleracea var. italica\tasparagus broccoli\t1\t1\tPLN\t36774\n",
+ "Brassica rapa\t\t1\t1\tPLN\t3711\n",
+ "Brassica rapa subsp. pekinensis\t\t1\t1\tPLN\t51351\n",
+ "Brucella abortus\t\t11\t0\tBCT\t235\n",
+ "Brugia malayi\t\t1\t5\tINV\t6279\n",
+ "Bruguiera gymnorhiza\t\t1\t1\tPLN\t39984\n",
+ "Bubalus bubalis\twater buffalo\t1\t2\tMAM\t89462\n",
+ "Burkholderia pseudomallei 112\t\t11\t0\tBCT\t441154\n",
+ "Burkholderia pseudomallei 14\t\t11\t0\tBCT\t441160\n",
+ "Burkholderia pseudomallei 381\t\t11\t0\tBCT\t441157\n",
+ "Burkholderia pseudomallei 7894\t\t11\t0\tBCT\t441156\n",
+ "Burkholderia pseudomallei 9\t\t11\t0\tBCT\t441158\n",
+ "Burkholderia pseudomallei 91\t\t11\t0\tBCT\t441159\n",
+ "Burkholderia pseudomallei B7210\t\t11\t0\tBCT\t441155\n",
+ "Burkholderia pseudomallei DM98\t\t11\t0\tBCT\t441161\n",
+ "Bursaphelenchus mucronatus\t\t1\t5\tINV\t6325\n",
+ "Bursaphelenchus xylophilus\t\t1\t5\tINV\t6326\n",
+ "Caenorhabditis brenneri\t\t1\t5\tINV\t135651\n",
+ "Caenorhabditis briggsae\t\t1\t5\tINV\t6238\n",
+ "Caenorhabditis briggsae AF16\t\t1\t5\tINV\t473542\n",
+ "Caenorhabditis elegans\t\t1\t5\tINV\t6239\n",
+ "Caenorhabditis remanei\t\t1\t5\tINV\t31234\n",
+ "Calanus finmarchicus\t\t1\t5\tINV\t6837\n",
+ "Callinectes sapidus\tblue crab\t1\t5\tINV\t6763\n",
+ "Callithrix jacchus\twhite-tufted-ear marmoset\t1\t2\tPRI\t9483\n",
+ "Callorhinchus milii\telephantfish\t1\t2\tVRT\t7868\n",
+ "Camellia sinensis\t\t1\t1\tPLN\t4442\n",
+ "Candida albicans\t\t12\t4\tPLN\t5476\n",
+ "Candida albicans SC5314\t\t12\t4\tPLN\t237561\n",
+ "Candida glabrata\t\t1\t3\tPLN\t5478\n",
+ "Candida glabrata CBS 138\t\t1\t3\tPLN\t284593\n",
+ "Candida parapsilosis\t\t12\t4\tPLN\t5480\n",
+ "Candida tropicalis\t\t12\t3\tPLN\t5482\n",
+ "candidate division TM7 single-cell isolate TM7a\t\t11\t0\tBCT\t447454\n",
+ "Canis latrans\tcoyote\t1\t2\tMAM\t9614\n",
+ "Canis lupus\tgray wolf\t1\t2\tMAM\t9612\n",
+ "Canis lupus familiaris\tdog\t1\t2\tMAM\t9615\n",
+ "Cannabis sativa\themp\t1\t1\tPLN\t3483\n",
+ "Capra hircus\tgoat\t1\t2\tMAM\t9925\n",
+ "Capsaspora owczarzaki\t\t1\t1\tINV\t192875\n",
+ "Capsicum annuum\t\t1\t1\tPLN\t4072\n",
+ "Carcinus maenas\tgreen crab\t1\t5\tINV\t6759\n",
+ "Carica papaya\tpapaya\t1\t1\tPLN\t3649\n",
+ "Carthamus tinctorius\tsafflower\t1\t1\tPLN\t4222\n",
+ "Catharanthus roseus\tMadagascar periwinkle\t1\t1\tPLN\t4058\n",
+ "Cavia porcellus\tdomestic guinea pig\t1\t2\tROD\t10141\n",
+ "Celuca pugilator\tAtlantic sand fiddler crab\t1\t5\tINV\t6772\n",
+ "Cenchrus ciliaris\t\t1\t1\tPLN\t35872\n",
+ "Centaurea maculosa\t\t1\t1\tPLN\t215693\n",
+ "Centaurea solstitialis\t\t1\t1\tPLN\t347529\n",
+ "Ceratodon purpureus\t\t1\t1\tPLN\t3225\n",
+ "Ceratopteris richardii\t\t1\t1\tPLN\t49495\n",
+ "Cercomonas longicauda\t\t1\t1\tINV\t100933\n",
+ "Chaetomium cupreum\t\t1\t4\tPLN\t155874\n",
+ "Chaetomium globosum CBS 148.51\t\t1\t4\tPLN\t306901\n",
+ "Chamaecyparis obtusa\t\t1\t1\tPLN\t13415\n",
+ "Chironomus tentans\t\t1\t5\tINV\t7153\n",
+ "Chlamydia trachomatis\t\t11\t0\tBCT\t813\n",
+ "Chlamydomonas incerta\t\t1\t1\tPLN\t51695\n",
+ "Chlamydomonas reinhardtii\t\t1\t1\tPLN\t3055\n",
+ "Chlamys farreri\t\t1\t5\tINV\t202578\n",
+ "Chlorocebus aethiops\tAfrican green monkey\t1\t2\tPRI\t9534\n",
+ "Chondrus crispus\tcarragheen\t1\t4\tPLN\t2769\n",
+ "Chrysemys picta\t\t1\t2\tVRT\t8479\n",
+ "Cicer arietinum\tchickpea\t1\t1\tPLN\t3827\n",
+ "Cichorium endivia\t\t1\t1\tPLN\t114280\n",
+ "Cichorium intybus\tchicory\t1\t1\tPLN\t13427\n",
+ "Ciona intestinalis\t\t1\t13\tINV\t7719\n",
+ "Ciona savignyi\t\t1\t13\tINV\t51511\n",
+ "Citrus aurantium\t\t1\t1\tPLN\t43166\n",
+ "Citrus clementina\t\t1\t1\tPLN\t85681\n",
+ "Citrus reshni\t\t1\t1\tPLN\t171252\n",
+ "Citrus reticulata\t\t1\t1\tPLN\t85571\n",
+ "Citrus sinensis\t\t1\t1\tPLN\t2711\n",
+ "Citrus unshiu\t\t1\t1\tPLN\t55188\n",
+ "Cleome hassleriana\t\t1\t1\tPLN\t28532\n",
+ "Clonorchis sinensis\t\t1\t9\tINV\t79923\n",
+ "Closterium peracerosum-strigosum-littorale complex\t\t1\t1\tPLN\t34146\n",
+ "Coccidioides immitis H538.4\t\t1\t4\tPLN\t396776\n",
+ "Coccidioides immitis RMSCC 3703\t\t1\t4\tPLN\t454286\n",
+ "Coccidioides immitis RS\t\t1\t4\tPLN\t246410\n",
+ "Coccidioides posadasii\t\t1\t4\tPLN\t199306\n",
+ "Coccidioides posadasii str. Silveira\t\t1\t4\tPLN\t443226\n",
+ "Coffea arabica\tcoffee\t1\t1\tPLN\t13443\n",
+ "Coffea canephora\t\t1\t1\tPLN\t49390\n",
+ "Coprinopsis cinerea\t\t1\t4\tPLN\t5346\n",
+ "Cordyceps bassiana\t\t1\t4\tPLN\t176275\n",
+ "Coregonus clupeaformis\tlake whitefish\t1\t2\tVRT\t59861\n",
+ "Corynascus heterothallicus\t\t1\t4\tPLN\t78579\n",
+ "Corynebacterium glutamicum\t\t11\t0\tBCT\t1718\n",
+ "Crassostrea gigas\tPacific oyster\t1\t5\tINV\t29159\n",
+ "Crassostrea virginica\teastern oyster\t1\t5\tINV\t6565\n",
+ "Cricetulus griseus\tChinese hamster\t1\t2\tROD\t10029\n",
+ "Crocus sativus\t\t1\t1\tPLN\t82528\n",
+ "Cryphonectria parasitica\t\t1\t4\tPLN\t5116\n",
+ "Cryptococcus laurentii\t\t1\t4\tPLN\t5418\n",
+ "Cryptococcus neoformans var. neoformans\t\t1\t4\tPLN\t40410\n",
+ "Cryptococcus neoformans var. neoformans B-3501A\t\t1\t4\tPLN\t283643\n",
+ "Cryptococcus neoformans var. neoformans JEC21\t\t1\t4\tPLN\t214684\n",
+ "Cryptomeria japonica\tJapanese cedar\t1\t1\tPLN\t3369\n",
+ "Cryptosporidium hominis TU502\t\t1\t4\tINV\t353151\n",
+ "Cryptosporidium parvum\t\t1\t4\tINV\t5807\n",
+ "Cryptosporidium parvum Iowa II\t\t1\t4\tINV\t353152\n",
+ "Ctenocephalides felis\tcat flea\t1\t5\tINV\t7515\n",
+ "Cucumis melo\tmuskmelon\t1\t1\tPLN\t3656\n",
+ "Cucumis melo subsp. agrestis\t\t1\t1\tPLN\t217619\n",
+ "Cucumis melo subsp. melo\t\t1\t1\tPLN\t412675\n",
+ "Cucumis sativus\tcucumber\t1\t1\tPLN\t3659\n",
+ "Culex pipiens quinquefasciatus\tsouthern house mosquito\t1\t5\tINV\t7176\n",
+ "Culicoides sonorensis\t\t1\t5\tINV\t179676\n",
+ "Cunninghamella elegans\t\t1\t4\tPLN\t4853\n",
+ "Curcuma longa\t\t1\t1\tPLN\t136217\n",
+ "Cyamopsis tetragonoloba\tguar\t1\t1\tPLN\t3832\n",
+ "Cyanidioschyzon merolae strain 10D\t\t1\t1\tPLN\t280699\n",
+ "Cyanophora paradoxa\t\t1\t1\tPLN\t2762\n",
+ "Cycas rumphii\t\t1\t1\tPLN\t58031\n",
+ "Cynodon dactylon\tBermuda grass\t1\t1\tPLN\t28909\n",
+ "Cyprinus carpio\tcommon carp\t1\t2\tVRT\t7962\n",
+ "Danio rerio\tzebrafish\t1\t2\tVRT\t7955\n",
+ "Daphnia magna\t\t1\t5\tINV\t35525\n",
+ "Dasypus novemcinctus\tnine-banded armadillo\t1\t2\tMAM\t9361\n",
+ "Debaryomyces hansenii CBS767\t\t1\t3\tPLN\t284592\n",
+ "Debaryomyces hansenii var. hansenii\t\t1\t3\tPLN\t58641\n",
+ "Deinagkistrodon acutus\t\t1\t2\tVRT\t36307\n",
+ "Dekkera bruxellensis\t\t1\t4\tPLN\t5007\n",
+ "Diabrotica virgifera virgifera\twestern corn rootworm\t1\t5\tINV\t50390\n",
+ "Diaphorina citri\tAsian citrus psyllid\t1\t5\tINV\t121845\n",
+ "Diaprepes abbreviatus\tDiaprepes root weevil\t1\t5\tINV\t13040\n",
+ "Dicentrarchus labrax\tEuropean sea bass\t1\t2\tVRT\t13489\n",
+ "Dictyocaulus viviparus\tbovine lungworm\t1\t5\tINV\t29172\n",
+ "Dictyostelium discoideum\t\t1\t1\tINV\t44689\n",
+ "Dictyostelium discoideum AX4\t\t1\t1\tINV\t352472\n",
+ "Diplonema papillatum\t\t1\t4\tINV\t91374\n",
+ "Dirofilaria immitis\tdog heartworm nematode\t1\t5\tINV\t6287\n",
+ "Drosophila ananassae\t\t1\t5\tINV\t7217\n",
+ "Drosophila auraria\t\t1\t5\tINV\t47315\n",
+ "Drosophila erecta\t\t1\t5\tINV\t7220\n",
+ "Drosophila grimshawi\t\t1\t5\tINV\t7222\n",
+ "Drosophila melanogaster\tfruit fly\t1\t5\tINV\t7227\n",
+ "Drosophila mojavensis\t\t1\t5\tINV\t7230\n",
+ "Drosophila persimilis\t\t1\t5\tINV\t7234\n",
+ "Drosophila pseudoobscura\t\t1\t5\tINV\t7237\n",
+ "Drosophila sechellia\t\t1\t5\tINV\t7238\n",
+ "Drosophila simulans\t\t1\t5\tINV\t7240\n",
+ "Drosophila virilis\t\t1\t5\tINV\t7244\n",
+ "Drosophila willistoni\t\t1\t5\tINV\t7260\n",
+ "Drosophila yakuba\t\t1\t5\tINV\t7245\n",
+ "Dugesia japonica\t\t1\t9\tINV\t6161\n",
+ "Dugesia ryukyuensis\t\t1\t9\tINV\t79738\n",
+ "Dunaliella salina\t\t1\t1\tPLN\t3046\n",
+ "Echinococcus granulosus\t\t1\t9\tINV\t6210\n",
+ "Echinops telfairi\tsmall Madagascar hedgehog\t1\t2\tMAM\t9371\n",
+ "Eimeria tenella\t\t1\t4\tINV\t5802\n",
+ "Eisenia fetida\tcommon brandling worm\t1\t5\tINV\t6396\n",
+ "Elaeis guineensis\tAfrican oil palm\t1\t1\tPLN\t51953\n",
+ "Elaeis oleifera\t\t1\t1\tPLN\t80265\n",
+ "Emericella nidulans\t\t1\t4\tPLN\t162425\n",
+ "Emiliania huxleyi\t\t1\t4\tPLN\t2903\n",
+ "Endoriftia persephone 'Hot96_1+Hot96_2'\t\t11\t0\tBCT\t394104\n",
+ "Entamoeba dispar\t\t1\t1\tINV\t46681\n",
+ "Entamoeba dispar SAW760\t\t1\t1\tINV\t370354\n",
+ "Entamoeba histolytica\t\t1\t1\tINV\t5759\n",
+ "Entamoeba histolytica HM-1:IMSS\t\t1\t1\tINV\t294381\n",
+ "Entamoeba invadens\t\t1\t1\tINV\t33085\n",
+ "Entamoeba invadens IP1\t\t1\t1\tINV\t370355\n",
+ "Entamoeba moshkovskii FIC\t\t1\t1\tINV\t434306\n",
+ "Entamoeba terrapinae\t\t1\t1\tINV\t110771\n",
+ "Epiphyas postvittana\t\t1\t5\tINV\t65032\n",
+ "Eptatretus burgeri\tinshore hagfish\t1\t2\tVRT\t7764\n",
+ "Equus caballus\thorse\t1\t2\tMAM\t9796\n",
+ "Eragrostis tef\t\t1\t1\tPLN\t110835\n",
+ "Erinaceus europaeus\twestern European hedgehog\t1\t2\tMAM\t9365\n",
+ "Escherichia coli\t\t11\t0\tBCT\t562\n",
+ "Eschscholzia californica\tCalifornia poppy\t1\t1\tPLN\t3467\n",
+ "Esox lucius\tnorthern pike\t1\t2\tVRT\t8010\n",
+ "Eubalaena glacialis\tNorth Atlantic right whale\t1\t2\tMAM\t27606\n",
+ "Eucalyptus camaldulensis\tMurray red gum\t1\t1\tPLN\t34316\n",
+ "Eucalyptus globulus subsp. bicostata\t\t1\t1\tPLN\t71272\n",
+ "Eucalyptus grandis\t\t1\t1\tPLN\t71139\n",
+ "Eucalyptus gunnii\tcider tree\t1\t1\tPLN\t3933\n",
+ "Euglena gracilis\t\t1\t4\tPLN\t3039\n",
+ "Euglena longa\t\t1\t4\tPLN\t3037\n",
+ "Euphorbia esula\tleafy spurge\t1\t1\tPLN\t3993\n",
+ "Euphorbia tirucalli\t\t1\t1\tPLN\t142860\n",
+ "Euprymna scolopes\t\t1\t5\tINV\t6613\n",
+ "Felis catus\tdomestic cat\t1\t2\tMAM\t9685\n",
+ "Fenneropenaeus chinensis\t\t1\t5\tINV\t139456\n",
+ "Festuca arundinacea\t\t1\t1\tPLN\t4606\n",
+ "Folsomia candida\t\t1\t5\tINV\t158441\n",
+ "fossil metagenome\t\t11\t2\tENV\t444079\n",
+ "Fragaria vesca\t\t1\t1\tPLN\t57918\n",
+ "Fragaria vesca subsp. vesca\t\t1\t1\tPLN\t101020\n",
+ "Fragilariopsis cylindrus\t\t1\t1\tPLN\t186039\n",
+ "Fundulus heteroclitus\tkillifish\t1\t2\tVRT\t8078\n",
+ "Fusarium oxysporum f. sp. cucumerinum\t\t1\t4\tPLN\t5508\n",
+ "Fusarium oxysporum f. sp. melonis\t\t1\t4\tPLN\t61369\n",
+ "Fusarium solani\t\t1\t4\tPLN\t169388\n",
+ "Fusarium sporotrichioides\t\t1\t4\tPLN\t5514\n",
+ "Fusarium virguliforme\t\t1\t4\tPLN\t232082\n",
+ "Gadus morhua\tAtlantic cod\t1\t2\tVRT\t8049\n",
+ "Gallus gallus\tchicken\t1\t2\tVRT\t9031\n",
+ "Gammarus pulex\t\t1\t5\tINV\t52641\n",
+ "Gasterosteus aculeatus\tthree-spined stickleback\t1\t2\tVRT\t69293\n",
+ "GB virus C\t\t1\t0\tVRL\t54290\n",
+ "Gekko japonicus\t\t1\t2\tVRT\t146911\n",
+ "Gene trapping vector VICTR75\t\t11\t0\tSYN\t447634\n",
+ "Gene trapping vector VICTR76\t\t11\t0\tSYN\t447635\n",
+ "Geomyces pannorum\t\t1\t4\tPLN\t79858\n",
+ "Gerbera hybrid cv. 'Terra Regina'\t\t1\t1\tPLN\t226891\n",
+ "Giardia intestinalis\t\t1\t0\tINV\t5741\n",
+ "Giardia lamblia ATCC 50803\t\t1\t0\tINV\t184922\n",
+ "Gibberella moniliformis\t\t1\t4\tPLN\t117187\n",
+ "Gibberella zeae\t\t1\t4\tPLN\t5518\n",
+ "Gibberella zeae PH-1\t\t1\t4\tPLN\t229533\n",
+ "Gillichthys mirabilis\tlong-jawed mudsucker\t1\t2\tVRT\t8222\n",
+ "Ginkgo biloba\tmaidenhair tree\t1\t1\tPLN\t3311\n",
+ "Glaucocystis nostochinearum\t\t1\t1\tPLN\t38271\n",
+ "Globodera pallida\t\t1\t5\tINV\t36090\n",
+ "Globodera rostochiensis\t\t1\t5\tINV\t31243\n",
+ "Gloeophyllum trabeum\t\t1\t4\tPLN\t104355\n",
+ "Glomus intraradices\t\t1\t4\tPLN\t4876\n",
+ "Glossina morsitans morsitans\t\t1\t5\tINV\t37546\n",
+ "Glycine max\tsoybean\t1\t1\tPLN\t3847\n",
+ "Glycine soja\t\t1\t1\tPLN\t3848\n",
+ "Glycyphagus domesticus\t\t1\t5\tINV\t105145\n",
+ "Gnetum gnemon\t\t1\t1\tPLN\t3382\n",
+ "Gobiocypris rarus\t\t1\t2\tVRT\t143606\n",
+ "Gorilla gorilla\tgorilla\t1\t2\tPRI\t9593\n",
+ "Gossypium arboreum\t\t1\t1\tPLN\t29729\n",
+ "Gossypium exiguum\t\t1\t1\tPLN\t47626\n",
+ "Gossypium herbaceum\t\t1\t1\tPLN\t34274\n",
+ "Gossypium hirsutum\tupland cotton\t1\t1\tPLN\t3635\n",
+ "Gossypium raimondii\t\t1\t1\tPLN\t29730\n",
+ "Gracilaria changii\t\t1\t4\tPLN\t172969\n",
+ "Graphocephala atropunctata\t\t1\t5\tINV\t36148\n",
+ "Grosmannia clavigera\t\t1\t4\tPLN\t226899\n",
+ "Gryllus bimaculatus\ttwo-spotted cricket\t1\t5\tINV\t6999\n",
+ "Guillardia theta\t\t1\t1\tPLN\t55529\n",
+ "Haemonchus contortus\t\t1\t5\tINV\t6289\n",
+ "Haemophilus influenzae\t\t11\t0\tBCT\t727\n",
+ "Halocynthia roretzi\t\t1\t13\tINV\t7729\n",
+ "Hartmannella vermiformis\t\t1\t1\tINV\t5778\n",
+ "Hebeloma cylindrosporum\t\t1\t4\tPLN\t76867\n",
+ "Hedyotis centranthoides\t\t1\t1\tPLN\t219666\n",
+ "Hedyotis terminalis\t\t1\t1\tPLN\t219667\n",
+ "Helianthus annuus\tcommon sunflower\t1\t1\tPLN\t4232\n",
+ "Helianthus argophyllus\t\t1\t1\tPLN\t73275\n",
+ "Helianthus ciliaris\t\t1\t1\tPLN\t73280\n",
+ "Helianthus exilis\t\t1\t1\tPLN\t400408\n",
+ "Helianthus paradoxus\t\t1\t1\tPLN\t73304\n",
+ "Helianthus petiolaris\t\t1\t1\tPLN\t4234\n",
+ "Helianthus tuberosus\t\t1\t1\tPLN\t4233\n",
+ "Helicobacter pylori\t\t11\t0\tBCT\t210\n",
+ "Heliconius erato\tcrimson-patched longwing\t1\t5\tINV\t33431\n",
+ "Heliconius melpomene\t\t1\t5\tINV\t34740\n",
+ "Hemicentrotus pulcherrimus\t\t1\t9\tINV\t7650\n",
+ "Hepatitis A virus\t\t1\t0\tVRL\t12092\n",
+ "Hepatitis B virus\t\t1\t0\tVRL\t10407\n",
+ "Hepatitis C virus\t\t1\t0\tVRL\t11103\n",
+ "Hepatitis C virus subtype 1a\t\t1\t0\tVRL\t31646\n",
+ "Hepatitis C virus subtype 1b\t\t1\t0\tVRL\t31647\n",
+ "Heterocapsa triquetra\t\t1\t4\tPLN\t66468\n",
+ "Heterodera glycines\t\t1\t5\tINV\t51029\n",
+ "Heterodera schachtii\t\t1\t5\tINV\t97005\n",
+ "Heterorhabditis bacteriophora\t\t1\t5\tINV\t37862\n",
+ "Hevea brasiliensis\t\t1\t1\tPLN\t3981\n",
+ "Hippoglossus hippoglossus\tAtlantic halibut\t1\t2\tVRT\t8267\n",
+ "Histiona aroides\t\t1\t1\tINV\t392300\n",
+ "Holothuria glaberrima\t\t1\t9\tINV\t31192\n",
+ "Homalodisca coagulata\tglassy-winged sharpshooter\t1\t5\tINV\t197043\n",
+ "Homarus americanus\tAmerican lobster\t1\t5\tINV\t6706\n",
+ "Homo sapiens\thuman\t1\t2\tPRI\t9606\n",
+ "Hordeum vulgare\t\t1\t1\tPLN\t4513\n",
+ "Hordeum vulgare subsp. spontaneum\t\t1\t1\tPLN\t77009\n",
+ "Hordeum vulgare subsp. vulgare\tdomesticated barley\t1\t1\tPLN\t112509\n",
+ "Human herpesvirus 5\tHuman cytomegalovirus\t1\t0\tVRL\t10359\n",
+ "Human immunodeficiency virus 1\t\t1\t0\tVRL\t11676\n",
+ "Human immunodeficiency virus 2\t\t1\t0\tVRL\t11709\n",
+ "Human metapneumovirus\t\t1\t0\tVRL\t162145\n",
+ "Human T-lymphotropic virus 1\t\t1\t0\tVRL\t11908\n",
+ "Humulus lupulus\tEuropean hop\t1\t1\tPLN\t3486\n",
+ "Hydra magnipapillata\t\t1\t4\tINV\t6085\n",
+ "Hydra vulgaris\t\t1\t4\tINV\t6087\n",
+ "Hydractinia echinata\t\t1\t4\tINV\t35630\n",
+ "Hyperamoeba dachnaya\t\t1\t1\tINV\t181200\n",
+ "Hypocrea jecorina\t\t1\t4\tPLN\t51453\n",
+ "Hypocrea lixii\t\t1\t4\tPLN\t5544\n",
+ "Hypocrea virens\t\t1\t4\tPLN\t29875\n",
+ "Hypsibius dujardini\t\t1\t5\tINV\t232323\n",
+ "Ichthyophthirius multifiliis\t\t6\t4\tINV\t5932\n",
+ "Ictalurus furcatus\tblue catfish\t1\t2\tVRT\t66913\n",
+ "Ictalurus punctatus\tchannel catfish\t1\t2\tVRT\t7998\n",
+ "Idiosepius paradoxus\t\t1\t5\tINV\t294707\n",
+ "Ipomoea batatas\tsweet potato\t1\t1\tPLN\t4120\n",
+ "Ipomoea nil\tJapanese morning glory\t1\t1\tPLN\t35883\n",
+ "Isochrysis galbana\t\t1\t1\tPLN\t37099\n",
+ "Ixodes scapularis\tblack-legged tick\t1\t5\tINV\t6945\n",
+ "Jakoba bahamiensis\t\t1\t1\tINV\t221721\n",
+ "Jakoba libera\t\t1\t1\tINV\t143017\n",
+ "Juglans regia\tEnglish walnut\t1\t1\tPLN\t51240\n",
+ "Karenia brevis\t\t1\t4\tPLN\t156230\n",
+ "Karlodinium micrum\t\t1\t4\tPLN\t342587\n",
+ "Kazachstania exigua\t\t1\t3\tPLN\t34358\n",
+ "Kazachstania unispora\t\t1\t3\tPLN\t27294\n",
+ "Kluyveromyces lactis\t\t1\t4\tPLN\t28985\n",
+ "Kluyveromyces lactis NRRL Y-1140\t\t1\t4\tPLN\t284590\n",
+ "Kluyveromyces marxianus\t\t1\t3\tPLN\t4911\n",
+ "Kluyveromyces thermotolerans\t\t1\t3\tPLN\t4916\n",
+ "Laccaria bicolor\t\t1\t4\tPLN\t29883\n",
+ "Lachancea kluyveri\t\t1\t3\tPLN\t4934\n",
+ "Lactuca perennis\t\t1\t1\tPLN\t43195\n",
+ "Lactuca saligna\t\t1\t1\tPLN\t75948\n",
+ "Lactuca sativa\t\t1\t1\tPLN\t4236\n",
+ "Lactuca serriola\t\t1\t1\tPLN\t75943\n",
+ "Lactuca virosa\t\t1\t1\tPLN\t75947\n",
+ "Lama pacos\talpaca\t1\t2\tMAM\t30538\n",
+ "Laminaria digitata\t\t1\t1\tPLN\t80365\n",
+ "Laupala kohalensis\t\t1\t5\tINV\t109027\n",
+ "Lawsonia intracellularis\t\t11\t0\tBCT\t29546\n",
+ "Leishmania braziliensis\t\t1\t4\tINV\t5660\n",
+ "Leishmania donovani chagasi\t\t1\t4\tINV\t44271\n",
+ "Leishmania infantum JPCM5\t\t1\t4\tINV\t435258\n",
+ "Leishmania major\t\t1\t4\tINV\t5664\n",
+ "Leishmania major strain Friedlin\t\t1\t4\tINV\t347515\n",
+ "Lentinula edodes\tshiitake mushroom\t1\t4\tPLN\t5353\n",
+ "Lepeophtheirus salmonis\tsalmon louse\t1\t5\tINV\t72036\n",
+ "Leptinotarsa decemlineata\tColorado potato beetle\t1\t5\tINV\t7539\n",
+ "Leucoraja erinacea\tlittle skate\t1\t2\tVRT\t7782\n",
+ "Leucosporidium scottii\t\t1\t4\tPLN\t5278\n",
+ "Limnanthes alba subsp. versicolor\t\t1\t1\tPLN\t377281\n",
+ "Limonium bicolor\t\t1\t1\tPLN\t293754\n",
+ "Lingulodinium polyedrum\t\t1\t4\tPLN\t160621\n",
+ "Linum usitatissimum\tflax\t1\t1\tPLN\t4006\n",
+ "Liriodendron tulipifera\t\t1\t1\tPLN\t3415\n",
+ "Listeria monocytogenes\t\t11\t0\tBCT\t1639\n",
+ "Listeria monocytogenes FSL F2-515\t\t11\t0\tBCT\t393116\n",
+ "Listeria monocytogenes FSL J1-208\t\t11\t0\tBCT\t393119\n",
+ "Lithognathus mormyrus\t\t1\t2\tVRT\t50591\n",
+ "Litomosoides sigmodontis\t\t1\t5\tINV\t42156\n",
+ "Litopenaeus vannamei\tPacific white shrimp\t1\t5\tINV\t6689\n",
+ "Locusta migratoria\tmigratory locust\t1\t5\tINV\t7004\n",
+ "Lodderomyces elongisporus NRRL YB-4239\t\t1\t3\tPLN\t379508\n",
+ "Lolium multiflorum\tItalian ryegrass\t1\t1\tPLN\t4521\n",
+ "Lolium temulentum\t\t1\t1\tPLN\t34176\n",
+ "Lotus japonicus\t\t1\t1\tPLN\t34305\n",
+ "Loxodonta africana\tAfrican savanna elephant\t1\t2\tMAM\t9785\n",
+ "Lumbricus rubellus\thumus earthworm\t1\t5\tINV\t35632\n",
+ "Lupinus albus\twhite lupine\t1\t1\tPLN\t3870\n",
+ "Lutzomyia longipalpis\t\t1\t5\tINV\t7200\n",
+ "Lycoris longituba\t\t1\t1\tPLN\t272140\n",
+ "Lysiphlebus testaceipes\t\t1\t5\tINV\t77504\n",
+ "Macaca fascicularis\tcrab-eating macaque\t1\t2\tPRI\t9541\n",
+ "Macaca mulatta\trhesus monkey\t1\t2\tPRI\t9544\n",
+ "Macaca nemestrina\tpig-tailed macaque\t1\t2\tPRI\t9545\n",
+ "Maconellicoccus hirsutus\thibiscus mealybug\t1\t5\tINV\t177089\n",
+ "Macropus eugenii\ttammar wallaby\t1\t2\tMAM\t9315\n",
+ "Macrostomum lignano\t\t1\t9\tINV\t282301\n",
+ "Magnaporthe grisea\t\t1\t4\tPLN\t148305\n",
+ "Magnaporthe grisea 70-15\t\t1\t4\tPLN\t242507\n",
+ "Magnetospirillum magnetotacticum MS-1\t\t11\t0\tBCT\t272627\n",
+ "Malawimonas californiana\t\t1\t1\tINV\t221722\n",
+ "Malawimonas jakobiformis\t\t1\t1\tINV\t136089\n",
+ "Manduca sexta\ttobacco hornworm\t1\t5\tINV\t7130\n",
+ "Manihot esculenta\tcassava\t1\t1\tPLN\t3983\n",
+ "Marchantia polymorpha\tliverwort\t1\t1\tPLN\t3197\n",
+ "marine metagenome\t\t11\t2\tENV\t408172\n",
+ "Marsupenaeus japonicus\t\t1\t5\tINV\t27405\n",
+ "Mastigamoeba balamuthi\t\t1\t1\tINV\t108607\n",
+ "Measles virus\t\t1\t0\tVRL\t11234\n",
+ "Medicago sativa\t\t1\t1\tPLN\t3879\n",
+ "Medicago truncatula\tbarrel medic\t1\t1\tPLN\t3880\n",
+ "Meleagris gallopavo\tturkey\t1\t2\tVRT\t9103\n",
+ "Meloidogyne arenaria\t\t1\t5\tINV\t6304\n",
+ "Meloidogyne chitwoodi\t\t1\t5\tINV\t59747\n",
+ "Meloidogyne hapla\t\t1\t5\tINV\t6305\n",
+ "Meloidogyne incognita\tsouthern root-knot nematode\t1\t5\tINV\t6306\n",
+ "Meloidogyne javanica\troot-knot nematode\t1\t5\tINV\t6303\n",
+ "Meloidogyne paranaensis\t\t1\t5\tINV\t189293\n",
+ "Mesembryanthemum crystallinum\tcommon iceplant\t1\t1\tPLN\t3544\n",
+ "Mesocricetus auratus\tgolden hamster\t1\t2\tROD\t10036\n",
+ "Mesostigma viride\t\t1\t1\tPLN\t41882\n",
+ "metagenome sequence\t\t11\t2\tENV\t256318\n",
+ "Metarhizium anisopliae\t\t1\t4\tPLN\t5530\n",
+ "Microbotryum violaceum\t\t1\t4\tPLN\t5272\n",
+ "Microcebus murinus\tgray mouse lemur\t1\t2\tPRI\t30608\n",
+ "Mimulus guttatus\tspotted monkey flower\t1\t1\tPLN\t4155\n",
+ "Mimulus lewisii\t\t1\t1\tPLN\t69919\n",
+ "Misgurnus anguillicaudatus\toriental weatherfish\t1\t2\tVRT\t75329\n",
+ "Molgula tectiformis\t\t1\t13\tINV\t30286\n",
+ "Monacrosporium haptotylum\t\t1\t4\tPLN\t74495\n",
+ "Monodelphis domestica\tgray short-tailed opossum\t1\t2\tMAM\t13616\n",
+ "Monosiga ovata\t\t1\t1\tINV\t81526\n",
+ "mouse gut metagenome\t\t11\t2\tENV\t410661\n",
+ "Mus musculus\thouse mouse\t1\t2\tROD\t10090\n",
+ "Mus musculus domesticus\twestern European house mouse\t1\t2\tROD\t10092\n",
+ "Mus musculus molossinus\tJapanese wild mouse\t1\t2\tROD\t57486\n",
+ "Musa acuminata\tdessert banana\t1\t1\tPLN\t4641\n",
+ "Mycobacterium tuberculosis\t\t11\t0\tBCT\t1773\n",
+ "Mycosphaerella graminicola\t\t1\t4\tPLN\t54734\n",
+ "Myotis lucifugus\tlittle brown bat\t1\t2\tMAM\t59463\n",
+ "Mytilus californianus\tCalifornia mussel\t1\t5\tINV\t6549\n",
+ "Mytilus galloprovincialis\tMediterranean mussel\t1\t5\tINV\t29158\n",
+ "Myzus persicae\tgreen peach aphid\t1\t5\tINV\t13164\n",
+ "Nakaseomyces delphensis\t\t1\t3\tPLN\t51657\n",
+ "Nasonia giraulti\t\t1\t5\tINV\t7426\n",
+ "Nasonia vitripennis\tjewel wasp\t1\t5\tINV\t7425\n",
+ "Necator americanus\t\t1\t5\tINV\t51031\n",
+ "Neisseria gonorrhoeae\t\t11\t0\tBCT\t485\n",
+ "Neisseria meningitidis\t\t11\t0\tBCT\t487\n",
+ "Nelumbo nucifera\t\t1\t1\tPLN\t4432\n",
+ "Nematostella vectensis\tstarlet sea anemone\t1\t4\tINV\t45351\n",
+ "Neosartorya fischeri NRRL 181\t\t1\t4\tPLN\t331117\n",
+ "Neospora caninum\t\t1\t4\tINV\t29176\n",
+ "Neovison vison\t\t1\t2\tMAM\t452646\n",
+ "Neurospora crassa\t\t1\t4\tPLN\t5141\n",
+ "Neurospora crassa OR74A\t\t1\t4\tPLN\t367110\n",
+ "Newcastle disease virus\t\t1\t0\tVRL\t11176\n",
+ "Nicotiana benthamiana\t\t1\t1\tPLN\t4100\n",
+ "Nicotiana sylvestris\twood tobacco\t1\t1\tPLN\t4096\n",
+ "Nicotiana tabacum\tcommon tobacco\t1\t1\tPLN\t4097\n",
+ "Nippostrongylus brasiliensis\t\t1\t5\tINV\t27835\n",
+ "Nuphar advena\t\t1\t1\tPLN\t77108\n",
+ "Ochotona princeps\tAmerican pika\t1\t2\tMAM\t9978\n",
+ "Ocimum basilicum\tsweet basil\t1\t1\tPLN\t39350\n",
+ "Onchocerca volvulus\t\t1\t5\tINV\t6282\n",
+ "Oncometopia nigricans\t\t1\t5\tINV\t266772\n",
+ "Oncorhynchus mykiss\trainbow trout\t1\t2\tVRT\t8022\n",
+ "Oncorhynchus nerka\tsockeye salmon\t1\t2\tVRT\t8023\n",
+ "Oncorhynchus tshawytscha\tChinook salmon\t1\t2\tVRT\t74940\n",
+ "Ophiostoma piliferum\t\t1\t4\tPLN\t38032\n",
+ "Opisthorchis viverrini\t\t1\t9\tINV\t6198\n",
+ "Oreochromis niloticus\tNile tilapia\t1\t2\tVRT\t8128\n",
+ "Ornithorhynchus anatinus\tplatypus\t1\t2\tMAM\t9258\n",
+ "Oryctolagus cuniculus\trabbit\t1\t2\tMAM\t9986\n",
+ "Oryza alta\t\t1\t1\tPLN\t52545\n",
+ "Oryza australiensis\t\t1\t1\tPLN\t4532\n",
+ "Oryza brachyantha\t\t1\t1\tPLN\t4533\n",
+ "Oryza coarctata\t\t1\t1\tPLN\t77588\n",
+ "Oryza glaberrima\tAfrican rice\t1\t1\tPLN\t4538\n",
+ "Oryza granulata\t\t1\t1\tPLN\t110450\n",
+ "Oryza minuta\t\t1\t1\tPLN\t63629\n",
+ "Oryza nivara\t\t1\t1\tPLN\t4536\n",
+ "Oryza officinalis\t\t1\t1\tPLN\t4535\n",
+ "Oryza punctata\t\t1\t1\tPLN\t4537\n",
+ "Oryza ridleyi\t\t1\t1\tPLN\t83308\n",
+ "Oryza rufipogon\t\t1\t1\tPLN\t4529\n",
+ "Oryza sativa\trice\t1\t1\tPLN\t4530\n",
+ "Oryza sativa Indica Group\t\t1\t1\tPLN\t39946\n",
+ "Oryza sativa Japonica Group\t\t1\t1\tPLN\t39947\n",
+ "Oryzias latipes\tJapanese medaka\t1\t2\tVRT\t8090\n",
+ "Oscarella carmela\t\t1\t4\tINV\t386100\n",
+ "Osmerus mordax\trainbow smelt\t1\t2\tVRT\t8014\n",
+ "Ostertagia ostertagi\t\t1\t5\tINV\t6317\n",
+ "Ostreococcus lucimarinus CCE9901\t\t1\t1\tPLN\t436017\n",
+ "Otolemur garnettii\tsmall-eared galago\t1\t2\tPRI\t30611\n",
+ "Ovis aries\tsheep\t1\t2\tMAM\t9940\n",
+ "Pan paniscus\tpygmy chimpanzee\t1\t2\tPRI\t9597\n",
+ "Pan troglodytes\tchimpanzee\t1\t2\tPRI\t9598\n",
+ "Pan troglodytes troglodytes\t\t1\t2\tPRI\t37011\n",
+ "Pan troglodytes verus\t\t1\t2\tPRI\t37012\n",
+ "Panax ginseng\t\t1\t1\tPLN\t4054\n",
+ "Panicum virgatum\tswitchgrass\t1\t1\tPLN\t38727\n",
+ "Paracentrotus lividus\tcommon urchin\t1\t9\tINV\t7656\n",
+ "Paracoccidioides brasiliensis\t\t1\t4\tPLN\t121759\n",
+ "Paralabidochromis chilotes\t\t1\t2\tVRT\t77306\n",
+ "Paralichthys olivaceus\tbastard halibut\t1\t2\tVRT\t8255\n",
+ "Paramecium tetraurelia\t\t6\t4\tINV\t5888\n",
+ "Parastrongyloides trichosuri\t\t1\t5\tINV\t131310\n",
+ "Pasteuria penetrans\t\t11\t0\tBCT\t86005\n",
+ "Patiria pectinifera\t\t1\t9\tINV\t7594\n",
+ "Pavlova lutheri\t\t1\t1\tPLN\t2832\n",
+ "Paxillus involutus\t\t1\t4\tPLN\t71150\n",
+ "Pediculus humanus capitis\thuman head louse\t1\t5\tINV\t121226\n",
+ "Pediculus humanus corporis\thuman body louse\t1\t5\tINV\t121224\n",
+ "Penaeus monodon\tblack tiger shrimp\t1\t5\tINV\t6687\n",
+ "Penicillium marneffei\t\t1\t4\tPLN\t37727\n",
+ "Pennisetum glaucum\t\t1\t1\tPLN\t4543\n",
+ "Perkinsus marinus ATCC 50983\t\t1\t4\tINV\t423536\n",
+ "Peromyscus maniculatus bairdii\tprairie deer mouse\t1\t2\tROD\t230844\n",
+ "Persea americana\tavocado\t1\t1\tPLN\t3435\n",
+ "Petromyzon marinus\tsea lamprey\t1\t2\tVRT\t7757\n",
+ "Phaeodactylum tricornutum\t\t1\t1\tPLN\t2850\n",
+ "Phaeosphaeria nodorum SN15\t\t1\t4\tPLN\t321614\n",
+ "Phakopsora pachyrhizi\t\t1\t4\tPLN\t170000\n",
+ "Phalaenopsis equestris\t\t1\t1\tPLN\t78828\n",
+ "Phalaenopsis violacea\t\t1\t1\tPLN\t86509\n",
+ "Phanerochaete chrysosporium\t\t1\t4\tPLN\t5306\n",
+ "Phaseolus coccineus\t\t1\t1\tPLN\t3886\n",
+ "Phaseolus vulgaris\t\t1\t1\tPLN\t3885\n",
+ "Phlebotomus papatasi\t\t1\t5\tINV\t29031\n",
+ "Photorhabdus luminescens\t\t11\t0\tBCT\t29488\n",
+ "Physarum polycephalum\tslime mold\t1\t1\tINV\t5791\n",
+ "Physcomitrella patens\t\t1\t1\tPLN\t3218\n",
+ "Physcomitrella patens subsp. patens\t\t1\t1\tPLN\t145481\n",
+ "Phytophthora brassicae\t\t1\t1\tPLN\t187813\n",
+ "Phytophthora infestans\tpotato late blight agent\t1\t1\tPLN\t4787\n",
+ "Phytophthora infestans T30-4\t\t1\t1\tPLN\t403677\n",
+ "Phytophthora parasitica\t\t1\t1\tPLN\t4792\n",
+ "Phytophthora ramorum\tSudden oak death agent\t1\t1\tPLN\t164328\n",
+ "Phytophthora sojae\t\t1\t1\tPLN\t67593\n",
+ "Picea abies\tNorway spruce\t1\t1\tPLN\t3329\n",
+ "Picea glauca\twhite spruce\t1\t1\tPLN\t3330\n",
+ "Picea sitchensis\tSitka spruce\t1\t1\tPLN\t3332\n",
+ "Pichia angusta\t\t1\t3\tPLN\t4905\n",
+ "Pichia farinosa\t\t1\t3\tPLN\t4920\n",
+ "Pichia guilliermondii ATCC 6260\t\t1\t3\tPLN\t294746\n",
+ "Pichia stipitis CBS 6054\t\t12\t3\tPLN\t322104\n",
+ "Pimephales promelas\t\t1\t2\tVRT\t90988\n",
+ "Pinus pinaster\t\t1\t1\tPLN\t71647\n",
+ "Pinus taeda\tloblolly pine\t1\t1\tPLN\t3352\n",
+ "Pisum sativum\tpea\t1\t1\tPLN\t3888\n",
+ "Plasmodium berghei\t\t1\t4\tINV\t5821\n",
+ "Plasmodium berghei strain ANKA\t\t1\t4\tINV\t5823\n",
+ "Plasmodium chabaudi\t\t1\t4\tINV\t5825\n",
+ "Plasmodium chabaudi chabaudi\t\t1\t4\tINV\t31271\n",
+ "Plasmodium falciparum\tmalaria parasite P. falciparum\t1\t4\tINV\t5833\n",
+ "Plasmodium falciparum 3D7\t\t1\t4\tINV\t36329\n",
+ "Plasmodium falciparum Dd2\t\t1\t4\tINV\t57267\n",
+ "Plasmodium falciparum HB3\t\t1\t4\tINV\t137071\n",
+ "Plasmodium vivax\tmalaria parasite P. vivax\t1\t4\tINV\t5855\n",
+ "Plasmodium yoelii\t\t1\t4\tINV\t5861\n",
+ "Plasmodium yoelii yoelii\t\t1\t4\tINV\t73239\n",
+ "Plasmodium yoelii yoelii str. 17XNL\t\t1\t4\tINV\t352914\n",
+ "Platichthys flesus\tEuropean flounder\t1\t2\tVRT\t8260\n",
+ "Plodia interpunctella\tIndianmeal moth\t1\t5\tINV\t58824\n",
+ "Pneumocystis carinii\t\t1\t4\tPLN\t4754\n",
+ "Podocoryne carnea\t\t1\t4\tINV\t6096\n",
+ "Poecilia reticulata\tguppy\t1\t2\tVRT\t8081\n",
+ "Polygonatum sibiricum\t\t1\t1\tPLN\t261423\n",
+ "Polysphondylium pallidum\t\t1\t1\tINV\t13642\n",
+ "Polytomella parva\t\t1\t1\tPLN\t51329\n",
+ "Poncirus trifoliata\t\t1\t1\tPLN\t37690\n",
+ "Pongo pygmaeus\torangutan\t1\t2\tPRI\t9600\n",
+ "Populus deltoides\t\t1\t1\tPLN\t3696\n",
+ "Populus euphratica\t\t1\t1\tPLN\t75702\n",
+ "Populus nigra\t\t1\t1\tPLN\t3691\n",
+ "Populus tremula\t\t1\t1\tPLN\t113636\n",
+ "Populus tremuloides\tquaking aspen\t1\t1\tPLN\t3693\n",
+ "Populus trichocarpa\t\t1\t1\tPLN\t3694\n",
+ "Porcine respiratory and reproductive syndrome virus\t\t1\t0\tVRL\t28344\n",
+ "Porphyra haitanensis\t\t1\t4\tPLN\t76159\n",
+ "Porphyra yezoensis\t\t1\t4\tPLN\t2788\n",
+ "Pratylenchus vulnus\t\t1\t5\tINV\t45931\n",
+ "Pristionchus pacificus\t\t1\t5\tINV\t54126\n",
+ "Prototheca wickerhamii\t\t1\t1\tPLN\t3111\n",
+ "Prunus armeniaca\tapricot\t1\t1\tPLN\t36596\n",
+ "Prunus dulcis\talmond\t1\t1\tPLN\t3755\n",
+ "Prunus persica\tpeach\t1\t1\tPLN\t3760\n",
+ "Prymnesium parvum\t\t1\t1\tPLN\t97485\n",
+ "Pseudomonas aeruginosa\t\t11\t0\tBCT\t287\n",
+ "Pseudotsuga menziesii\tDouglas-fir\t1\t1\tPLN\t3357\n",
+ "Pseudotsuga menziesii var. menziesii\t\t1\t1\tPLN\t278161\n",
+ "Psychroflexus torquis ATCC 700755\t\t11\t0\tBCT\t313595\n",
+ "Puccinellia tenuiflora\t\t1\t1\tPLN\t240906\n",
+ "Puccinia graminis f. sp. tritici CRL 75-36-700-3\t\t1\t4\tPLN\t418459\n",
+ "Puccinia triticina\t\t1\t4\tPLN\t208348\n",
+ "Pythium ultimum DAOM BR144\t\t1\t1\tPLN\t431595\n",
+ "Rabies virus\t\t1\t0\tVRL\t11292\n",
+ "Raphanus raphanistrum subsp. landra\t\t1\t1\tPLN\t328428\n",
+ "Raphanus raphanistrum subsp. maritimus\t\t1\t1\tPLN\t457179\n",
+ "Raphanus raphanistrum subsp. raphanistrum\t\t1\t1\tPLN\t109997\n",
+ "Raphanus sativus\tradish\t1\t1\tPLN\t3726\n",
+ "Raphanus sativus var. oleiformis\t\t1\t1\tPLN\t463157\n",
+ "Rattus norvegicus\tNorway rat\t1\t2\tROD\t10116\n",
+ "Reclinomonas americana\t\t1\t1\tINV\t48483\n",
+ "Rhipicephalus appendiculatus\t\t1\t5\tINV\t34631\n",
+ "Rhipicephalus microplus\tsouthern cattle tick\t1\t5\tINV\t6941\n",
+ "Rhizopus oryzae\t\t1\t1\tPLN\t64495\n",
+ "Rhodnius prolixus\t\t1\t5\tINV\t13249\n",
+ "Rhynchosciara americana\t\t1\t5\tINV\t7186\n",
+ "Ricinus communis\tcastor bean\t1\t1\tPLN\t3988\n",
+ "Robinia pseudoacacia\t\t1\t1\tPLN\t35938\n",
+ "Rosa hybrid cultivar\t\t1\t1\tPLN\t128735\n",
+ "Rutilus rutilus\troach minnow\t1\t2\tVRT\t48668\n",
+ "Saccharomyces castellii\t\t1\t3\tPLN\t27288\n",
+ "Saccharomyces cerevisiae\tbaker's yeast\t1\t3\tPLN\t4932\n",
+ "Saccharomyces mikatae IFO 1815\t\t1\t3\tPLN\t226126\n",
+ "Saccharomyces pastorianus\t\t1\t3\tPLN\t27292\n",
+ "Saccharomyces servazzii\t\t1\t3\tPLN\t27293\n",
+ "Saccharomyces uvarum\t\t1\t3\tPLN\t230603\n",
+ "Saccharum hybrid cultivar\t\t1\t1\tPLN\t128810\n",
+ "Saccharum officinarum\t\t1\t1\tPLN\t4547\n",
+ "Saccoglossus kowalevskii\t\t1\t9\tINV\t10224\n",
+ "Saitoella complicata\t\t1\t4\tPLN\t5606\n",
+ "Salmo salar\tAtlantic salmon\t1\t2\tVRT\t8030\n",
+ "Salvelinus fontinalis\tbrook trout\t1\t2\tVRT\t8038\n",
+ "Salvia miltiorrhiza\t\t1\t1\tPLN\t226208\n",
+ "Sarcocystis falcatula\t\t1\t4\tINV\t32593\n",
+ "Sarcocystis neurona\t\t1\t4\tINV\t42890\n",
+ "Saruma henryi\t\t1\t1\tPLN\t13258\n",
+ "Sawyeria marylandensis\t\t1\t1\tINV\t194530\n",
+ "Scenedesmus obliquus\t\t1\t22\tPLN\t3088\n",
+ "Schistosoma japonicum\t\t1\t9\tINV\t6182\n",
+ "Schistosoma mansoni\t\t1\t9\tINV\t6183\n",
+ "Schizosaccharomyces pombe\tfission yeast\t1\t4\tPLN\t4896\n",
+ "Schizosaccharomyces pombe 972h-\t\t1\t4\tPLN\t284812\n",
+ "Schmidtea mediterranea\t\t1\t9\tINV\t79327\n",
+ "Sclerotinia sclerotiorum\t\t1\t4\tPLN\t5180\n",
+ "Sclerotinia sclerotiorum 1980\t\t1\t4\tPLN\t325569\n",
+ "Sebastes rastrelliger\tgrass rockfish\t1\t2\tVRT\t72095\n",
+ "Secale cereale\trye\t1\t1\tPLN\t4550\n",
+ "Seculamonas ecuadoriensis\t\t1\t1\tINV\t221724\n",
+ "Selaginella lepidophylla\t\t1\t1\tPLN\t59777\n",
+ "Sesamum indicum\tsesame\t1\t1\tPLN\t4182\n",
+ "Simian immunodeficiency virus\t\t1\t0\tVRL\t11723\n",
+ "Solanum chacoense\tChaco potato\t1\t1\tPLN\t4108\n",
+ "Solanum habrochaites\t\t1\t1\tPLN\t62890\n",
+ "Solanum lycopersicum\t\t1\t1\tPLN\t4081\n",
+ "Solanum pennellii\t\t1\t1\tPLN\t28526\n",
+ "Solanum tuberosum\tpotato\t1\t1\tPLN\t4113\n",
+ "Solenopsis invicta\tred fire ant\t1\t5\tINV\t13686\n",
+ "Sorex araneus\tEuropean shrew\t1\t2\tMAM\t42254\n",
+ "Sorghum bicolor\tsorghum\t1\t1\tPLN\t4558\n",
+ "Sorghum propinquum\t\t1\t1\tPLN\t132711\n",
+ "Sparus aurata\tgilthead seabream\t1\t2\tVRT\t8175\n",
+ "Spermophilus lateralis\tgolden-mantled ground squirrel\t1\t2\tROD\t76772\n",
+ "Spermophilus tridecemlineatus\tthirteen-lined ground squirrel\t1\t2\tROD\t43179\n",
+ "Sphaeroforma arctica\t\t1\t1\tINV\t72019\n",
+ "Spironucleus barkhanus\t\t6\t0\tINV\t103874\n",
+ "Spizellomyces punctatus\t\t1\t16\tPLN\t109760\n",
+ "Spodoptera frugiperda\tfall armyworm\t1\t5\tINV\t7108\n",
+ "Squalus acanthias\tspiny dogfish\t1\t2\tVRT\t7797\n",
+ "Stachyamoeba lipophora\t\t1\t1\tINV\t463046\n",
+ "Staphylococcus aureus\t\t11\t0\tBCT\t1280\n",
+ "Staphylococcus epidermidis\t\t11\t0\tBCT\t1282\n",
+ "Sterkiella histriomuscorum\t\t6\t4\tINV\t94289\n",
+ "Stevia rebaudiana\t\t1\t1\tPLN\t55670\n",
+ "Streblomastix strix\t\t6\t1\tINV\t222440\n",
+ "Streptococcus agalactiae\t\t11\t0\tBCT\t1311\n",
+ "Streptococcus pneumoniae\t\t11\t0\tBCT\t1313\n",
+ "Streptococcus pyogenes\t\t11\t0\tBCT\t1314\n",
+ "Strongylocentrotus purpuratus\t\t1\t9\tINV\t7668\n",
+ "Strongyloides ratti\t\t1\t5\tINV\t34506\n",
+ "Strongyloides stercoralis\t\t1\t5\tINV\t6248\n",
+ "Suidasia medanensis\t\t1\t5\tINV\t223625\n",
+ "Sus scrofa\tpig\t1\t2\tMAM\t9823\n",
+ "Taenia solium\tpork tapeworm\t1\t9\tINV\t6204\n",
+ "Taeniopygia guttata\t\t1\t2\tVRT\t59729\n",
+ "Taiwania cryptomerioides\t\t1\t1\tPLN\t50187\n",
+ "Takifugu rubripes\ttorafugu\t1\t2\tVRT\t31033\n",
+ "Tamarix androssowii\t\t1\t1\tPLN\t189785\n",
+ "Tamarix hispida\t\t1\t1\tPLN\t189793\n",
+ "Taphrina deformans\tpeach leaf curl fungus\t1\t4\tPLN\t5011\n",
+ "Taraxacum kok-saghyz\t\t1\t1\tPLN\t333970\n",
+ "Taraxacum officinale\t\t1\t1\tPLN\t50225\n",
+ "Teladorsagia circumcincta\t\t1\t5\tINV\t45464\n",
+ "Tetrahymena thermophila\t\t6\t4\tINV\t5911\n",
+ "Tetrahymena thermophila SB210\t\t6\t4\tINV\t312017\n",
+ "Tetraodon nigroviridis\t\t1\t2\tVRT\t99883\n",
+ "Thalassiosira pseudonana CCMP1335\t\t1\t4\tPLN\t296543\n",
+ "Theileria annulata\t\t1\t4\tINV\t5874\n",
+ "Theileria annulata strain Ankara\t\t1\t4\tINV\t353154\n",
+ "Theileria parva\t\t1\t4\tINV\t5875\n",
+ "Theileria parva strain Muguga\t\t1\t4\tINV\t333668\n",
+ "Thellungiella halophila\t\t1\t1\tPLN\t98038\n",
+ "Thellungiella salsuginea\t\t1\t1\tPLN\t72664\n",
+ "Theobroma cacao\tcacao\t1\t1\tPLN\t3641\n",
+ "Thermomyces lanuginosus\t\t1\t4\tPLN\t5541\n",
+ "Thlaspi caerulescens\t\t1\t1\tPLN\t107243\n",
+ "Thunnus thynnus\tbluefin tuna\t1\t2\tVRT\t8237\n",
+ "Thymallus arcticus\tArctic grayling\t1\t2\tVRT\t70285\n",
+ "Torque teno virus\t\t1\t0\tVRL\t68887\n",
+ "Tortula ruralis\t\t1\t1\tPLN\t38588\n",
+ "Toxocara canis\t\t1\t5\tINV\t6265\n",
+ "Toxoplasma gondii\t\t1\t4\tINV\t5811\n",
+ "Toxoplasma gondii RH\t\t1\t4\tINV\t383379\n",
+ "Toxoptera citricida\tbrown citrus aphid\t1\t5\tINV\t223852\n",
+ "Trametes versicolor\t\t1\t4\tPLN\t5325\n",
+ "Tribolium castaneum\tred flour beetle\t1\t5\tINV\t7070\n",
+ "Trichinella spiralis\t\t1\t5\tINV\t6334\n",
+ "Trichoderma reesei QM6a\t\t1\t4\tPLN\t431241\n",
+ "Trichomonas vaginalis\t\t1\t0\tINV\t5722\n",
+ "Trichomonas vaginalis G3\t\t1\t0\tINV\t412133\n",
+ "Trichophyton rubrum\t\t1\t4\tPLN\t5551\n",
+ "Trichosurus vulpecula\tsilver-gray brushtail possum\t1\t2\tMAM\t9337\n",
+ "Trichuris muris\t\t1\t5\tINV\t70415\n",
+ "Trichuris vulpis\t\t1\t5\tINV\t219738\n",
+ "Trifolium pratense\t\t1\t1\tPLN\t57577\n",
+ "Trifolium repens\twhite clover\t1\t1\tPLN\t3899\n",
+ "Trimastix pyriformis\t\t1\t1\tINV\t342808\n",
+ "Triphysaria versicolor\t\t1\t1\tPLN\t64093\n",
+ "Triticum aestivum\tbread wheat\t1\t1\tPLN\t4565\n",
+ "Triticum monococcum\t\t1\t1\tPLN\t4568\n",
+ "Triticum turgidum subsp. durum\tdurum wheat\t1\t1\tPLN\t4567\n",
+ "Tritrichomonas foetus\t\t1\t0\tINV\t5724\n",
+ "Trypanosoma brucei\t\t1\t4\tINV\t5691\n",
+ "Trypanosoma brucei rhodesiense\t\t1\t4\tINV\t31286\n",
+ "Trypanosoma brucei TREU927\t\t1\t4\tINV\t185431\n",
+ "Trypanosoma cruzi\t\t1\t4\tINV\t5693\n",
+ "Trypanosoma cruzi strain CL Brener\t\t1\t4\tINV\t353153\n",
+ "Tuber borchii\twhitish truffle\t1\t4\tPLN\t42251\n",
+ "Tupaia belangeri\tnorthern tree shrew\t1\t2\tMAM\t37347\n",
+ "Tursiops truncatus\tbottlenosed dolphin\t1\t2\tMAM\t9739\n",
+ "uncultured archaeon\t\t11\t0\tENV\t115547\n",
+ "uncultured bacterium\t\t11\t0\tENV\t77133\n",
+ "uncultured eukaryote\t\t1\t1\tENV\t100272\n",
+ "uncultured fungus\t\t1\t4\tENV\t175245\n",
+ "uncultured marine virus\t\t1\t0\tENV\t186617\n",
+ "uncultured organism\t\t11\t2\tENV\t155900\n",
+ "uncultured prokaryote\t\t11\t0\tENV\t198431\n",
+ "Uromyces appendiculatus\t\t1\t4\tPLN\t5264\n",
+ "Ustilago maydis\t\t1\t4\tPLN\t5270\n",
+ "Ustilago maydis 521\t\t1\t4\tPLN\t237631\n",
+ "Vaccinium corymbosum\t\t1\t1\tPLN\t69266\n",
+ "Vanderwaltozyma polyspora DSM 70294\t\t1\t3\tPLN\t436907\n",
+ "Verticillium dahliae\t\t1\t4\tPLN\t27337\n",
+ "Vibrio parahaemolyticus AQ3810\t\t11\t0\tBCT\t419109\n",
+ "Vigna unguiculata\tcowpea\t1\t1\tPLN\t3917\n",
+ "Vitis hybrid cultivar\t\t1\t1\tPLN\t241073\n",
+ "Vitis shuttleworthii\t\t1\t1\tPLN\t246827\n",
+ "Vitis vinifera\t\t1\t1\tPLN\t29760\n",
+ "Welwitschia mirabilis\t\t1\t1\tPLN\t3377\n",
+ "Wuchereria bancrofti\t\t1\t5\tINV\t6293\n",
+ "Xenopus laevis\tAfrican clawed frog\t1\t2\tVRT\t8355\n",
+ "Xenopus tropicalis\twestern clawed frog\t1\t2\tVRT\t8364\n",
+ "Xiphinema index\t\t1\t5\tINV\t46003\n",
+ "Yarrowia lipolytica\t\t1\t3\tPLN\t4952\n",
+ "Yarrowia lipolytica CLIB122\t\t1\t3\tPLN\t284591\n",
+ "Zamia fischeri\t\t1\t1\tPLN\t34342\n",
+ "Zantedeschia aethiopica\t\t1\t1\tPLN\t69721\n",
+ "Zea mays\t\t1\t1\tPLN\t4577\n",
+ "Zea mays subsp. mays\tmaize\t1\t1\tPLN\t381124\n",
+ "Zea mays subsp. parviglumis\t\t1\t1\tPLN\t76912\n",
+ "Zingiber officinale\t\t1\t1\tPLN\t94328\n",
+ "Zinnia elegans\t\t1\t1\tPLN\t34245\n",
+ "Zostera marina\t\t1\t1\tPLN\t29655\n",
+ "Zygosaccharomyces rouxii\t\t1\t3\tPLN\t4956\n",
+ NULL
+};
+#endif
+
extern Boolean LoadOrganismTable (void)
{
@@ -169,9 +1006,10 @@ extern Boolean LoadOrganismTable (void)
Boolean failed;
Char first [16];
Int2 idx;
+ CharPtr lst;
Int8 len;
Int2 num;
- CharPtr ptr;
+ CharPtr ptr = NULL;
Char str [PATH_MAX];
CharPtr tmp;
Int2 version;
@@ -188,9 +1026,9 @@ extern Boolean LoadOrganismTable (void)
orgNum = 0;
failed = TRUE;
ProgramPath (str, sizeof (str));
- ptr = StringRChr (str, DIRDELIMCHR);
- if (ptr != NULL) {
- *ptr = '\0';
+ tmp = StringRChr (str, DIRDELIMCHR);
+ if (tmp != NULL) {
+ *tmp = '\0';
FileBuildPath (str, NULL, "taxlist.txt");
len = FileLength (str);
f = FileOpen (str, "r");
@@ -204,7 +1042,6 @@ extern Boolean LoadOrganismTable (void)
if (f != NULL) {
ptr = MemNew ((size_t) (len + 5));
if (ptr != NULL) {
- orgTxtPtr = ptr;
FileRead (ptr, (size_t) len, 1, f);
#if (defined(OS_DOS) || defined (OS_NT))
p = ptr;
@@ -229,51 +1066,77 @@ extern Boolean LoadOrganismTable (void)
p++;
}
#endif
- tmp = ptr;
- ch = *tmp;
- while (ch != '\0' && ch != '\n') {
+ }
+ FileClose (f);
+ }
+ }
+ if (ptr == NULL) {
+#ifndef WIN16
+ idx = 0;
+ len = 0;
+ tmp = taxlistMemStrs [idx];
+ while (tmp != NULL) {
+ len += StringLen (tmp);
+ idx++;
+ tmp = taxlistMemStrs [idx];
+ }
+ ptr = MemNew ((size_t) (len + 5));
+ if (ptr != NULL) {
+ lst = ptr;
+ idx = 0;
+ tmp = taxlistMemStrs [idx];
+ while (tmp != NULL) {
+ lst = StringMove (lst, tmp);
+ idx++;
+ tmp = taxlistMemStrs [idx];
+ }
+ }
+#endif
+ }
+ if (ptr != NULL) {
+ orgTxtPtr = ptr;
+ tmp = ptr;
+ ch = *tmp;
+ while (ch != '\0' && ch != '\n') {
+ tmp++;
+ ch = *tmp;
+ }
+ *tmp = '\0';
+ StringNCpy_0 (first, ptr, sizeof (first) - 1);
+ *tmp = ch;
+ if (StrToInt (first, &version)) {
+ tmp++;
+ ptr = tmp;
+ }
+ num = 0;
+ tmp = ptr;
+ ch = *tmp;
+ while (ch != '\0') {
+ if (ch == '\n') {
+ num++;
+ }
+ tmp++;
+ ch = *tmp;
+ }
+ orgStrIdx = MemNew (sizeof (CharPtr) * (size_t) (num + 3));
+ if (orgStrIdx != NULL) {
+ idx = 0;
+ tmp = ptr;
+ ch = *tmp;
+ orgStrIdx [idx] = tmp;
+ while (ch != '\0') {
+ if (ch == '\n') {
+ idx++;
tmp++;
ch = *tmp;
- }
- *tmp = '\0';
- StringNCpy_0 (first, ptr, sizeof (first) - 1);
- *tmp = ch;
- if (StrToInt (first, &version)) {
- tmp++;
- ptr = tmp;
- }
- num = 0;
- tmp = ptr;
- ch = *tmp;
- while (ch != '\0') {
- if (ch == '\n') {
- num++;
- }
+ orgStrIdx [idx] = tmp;
+ } else {
tmp++;
ch = *tmp;
}
- orgStrIdx = MemNew (sizeof (CharPtr) * (size_t) (num + 3));
- if (orgStrIdx != NULL) {
- idx = 0;
- tmp = ptr;
- ch = *tmp;
- orgStrIdx [idx] = tmp;
- while (ch != '\0') {
- if (ch == '\n') {
- idx++;
- tmp++;
- ch = *tmp;
- orgStrIdx [idx] = tmp;
- } else {
- tmp++;
- ch = *tmp;
- }
- }
- orgNum = num;
- failed = FALSE;
- }
}
- FileClose (f);
+ orgNum = num;
+ failed = FALSE;
}
}
if (failed) {
@@ -1729,7 +2592,7 @@ static void FixModifierTextMove (ButtoN b)
fp->remove = FALSE;
fp->move_to_text = TRUE;
fp->do_all = FALSE;
- fp->done = TRUE;
+ fp->done = TRUE;
}
static void FixModifierTextMoveAll (ButtoN b)
@@ -1743,7 +2606,7 @@ static void FixModifierTextMoveAll (ButtoN b)
fp->remove = FALSE;
fp->move_to_text = TRUE;
fp->do_all = TRUE;
- fp->done = TRUE;
+ fp->done = TRUE;
}
static void FixModifierTextRemove (ButtoN b)
@@ -1757,7 +2620,7 @@ static void FixModifierTextRemove (ButtoN b)
fp->remove = TRUE;
fp->move_to_text = FALSE;
fp->do_all = FALSE;
- fp->done = TRUE;
+ fp->done = TRUE;
}
static void FixModifierTextRemoveAll (ButtoN b)
@@ -1771,7 +2634,7 @@ static void FixModifierTextRemoveAll (ButtoN b)
fp->remove = TRUE;
fp->move_to_text = FALSE;
fp->do_all = TRUE;
- fp->done = TRUE;
+ fp->done = TRUE;
}
extern ModTextFixPtr ModTextFixNew (void)
@@ -1807,78 +2670,78 @@ GetModifierTextFix (ModTextFixPtr tfp, Uint1 subtype, CharPtr txt)
if (tfp == NULL) return;
switch (subtype)
{
- case SUBSRC_rearranged:
- if (tfp->remove_all_rearranged)
- {
- tfp->remove_this = TRUE;
- tfp->move_this = FALSE;
- return;
- }
- else if (tfp->move_all_rearranged)
- {
- tfp->move_this = TRUE;
- tfp->remove_this = FALSE;
- return;
- }
- break;
- case SUBSRC_transgenic:
- if (tfp->remove_all_transgenic)
- {
- tfp->remove_this = TRUE;
- tfp->move_this = FALSE;
- return;
- }
- else if (tfp->move_all_transgenic)
- {
- tfp->move_this = TRUE;
- tfp->remove_this = FALSE;
- return;
- }
- break;
- case SUBSRC_germline:
- if (tfp->remove_all_germline)
- {
- tfp->remove_this = TRUE;
- tfp->move_this = FALSE;
- return;
- }
- else if (tfp->move_all_germline)
- {
- tfp->move_this = TRUE;
- tfp->remove_this = FALSE;
- return;
- }
- break;
- case SUBSRC_environmental_sample:
- if (tfp->remove_all_environmental)
- {
- tfp->remove_this = TRUE;
- tfp->move_this = FALSE;
- return;
- }
- else if (tfp->move_all_environmental)
- {
- tfp->move_this = TRUE;
- tfp->remove_this = FALSE;
- return;
- }
- break;
- case SUBSRC_metagenomic:
- if (tfp->remove_all_metagenomic)
- {
- tfp->remove_this = TRUE;
- tfp->move_this = FALSE;
- return;
- }
- else if (tfp->move_all_metagenomic)
- {
- tfp->move_this = TRUE;
- tfp->remove_this = FALSE;
- return;
- }
- break;
- default:
- break;
+ case SUBSRC_rearranged:
+ if (tfp->remove_all_rearranged)
+ {
+ tfp->remove_this = TRUE;
+ tfp->move_this = FALSE;
+ return;
+ }
+ else if (tfp->move_all_rearranged)
+ {
+ tfp->move_this = TRUE;
+ tfp->remove_this = FALSE;
+ return;
+ }
+ break;
+ case SUBSRC_transgenic:
+ if (tfp->remove_all_transgenic)
+ {
+ tfp->remove_this = TRUE;
+ tfp->move_this = FALSE;
+ return;
+ }
+ else if (tfp->move_all_transgenic)
+ {
+ tfp->move_this = TRUE;
+ tfp->remove_this = FALSE;
+ return;
+ }
+ break;
+ case SUBSRC_germline:
+ if (tfp->remove_all_germline)
+ {
+ tfp->remove_this = TRUE;
+ tfp->move_this = FALSE;
+ return;
+ }
+ else if (tfp->move_all_germline)
+ {
+ tfp->move_this = TRUE;
+ tfp->remove_this = FALSE;
+ return;
+ }
+ break;
+ case SUBSRC_environmental_sample:
+ if (tfp->remove_all_environmental)
+ {
+ tfp->remove_this = TRUE;
+ tfp->move_this = FALSE;
+ return;
+ }
+ else if (tfp->move_all_environmental)
+ {
+ tfp->move_this = TRUE;
+ tfp->remove_this = FALSE;
+ return;
+ }
+ break;
+ case SUBSRC_metagenomic:
+ if (tfp->remove_all_metagenomic)
+ {
+ tfp->remove_this = TRUE;
+ tfp->move_this = FALSE;
+ return;
+ }
+ else if (tfp->move_all_metagenomic)
+ {
+ tfp->move_this = TRUE;
+ tfp->remove_this = FALSE;
+ return;
+ }
+ break;
+ default:
+ break;
}
fd.w = ModalWindow(-20, -13, -10, -10, NULL);
@@ -1889,21 +2752,21 @@ GetModifierTextFix (ModTextFixPtr tfp, Uint1 subtype, CharPtr txt)
if (prompt_str == NULL) return;
switch (subtype)
{
- case SUBSRC_rearranged:
- sprintf (prompt_str, prompt_fmt, txt, "a rearranged");
- break;
- case SUBSRC_germline:
- sprintf (prompt_str, prompt_fmt, txt, "a germline");
- break;
- case SUBSRC_transgenic:
- sprintf (prompt_str, prompt_fmt, txt, "a transgenic");
- break;
- case SUBSRC_environmental_sample:
- sprintf (prompt_str, prompt_fmt, txt, "an environmental sample");
- break;
- case SUBSRC_metagenomic:
- sprintf (prompt_str, prompt_fmt, txt, "a metagenomic");
- break;
+ case SUBSRC_rearranged:
+ sprintf (prompt_str, prompt_fmt, txt, "a rearranged");
+ break;
+ case SUBSRC_germline:
+ sprintf (prompt_str, prompt_fmt, txt, "a germline");
+ break;
+ case SUBSRC_transgenic:
+ sprintf (prompt_str, prompt_fmt, txt, "a transgenic");
+ break;
+ case SUBSRC_environmental_sample:
+ sprintf (prompt_str, prompt_fmt, txt, "an environmental sample");
+ break;
+ case SUBSRC_metagenomic:
+ sprintf (prompt_str, prompt_fmt, txt, "a metagenomic");
+ break;
}
t = HiddenGroup (g, 1, 0, NULL);
@@ -1934,63 +2797,63 @@ GetModifierTextFix (ModTextFixPtr tfp, Uint1 subtype, CharPtr txt)
if (fd.remove)
{
- tfp->remove_this = TRUE;
- if (fd.do_all)
- {
- switch (subtype)
- {
- case SUBSRC_rearranged:
- tfp->remove_all_rearranged = TRUE;
- tfp->move_all_rearranged = FALSE;
- break;
- case SUBSRC_transgenic:
- tfp->remove_all_transgenic = TRUE;
- tfp->move_all_transgenic = FALSE;
- break;
- case SUBSRC_germline:
- tfp->remove_all_germline = TRUE;
- tfp->move_all_germline = FALSE;
- break;
- case SUBSRC_environmental_sample:
- tfp->remove_all_environmental = TRUE;
- tfp->move_all_environmental = FALSE;
- break;
- case SUBSRC_metagenomic:
- tfp->remove_all_metagenomic = TRUE;
- tfp->move_all_metagenomic = FALSE;
- break;
- }
- }
+ tfp->remove_this = TRUE;
+ if (fd.do_all)
+ {
+ switch (subtype)
+ {
+ case SUBSRC_rearranged:
+ tfp->remove_all_rearranged = TRUE;
+ tfp->move_all_rearranged = FALSE;
+ break;
+ case SUBSRC_transgenic:
+ tfp->remove_all_transgenic = TRUE;
+ tfp->move_all_transgenic = FALSE;
+ break;
+ case SUBSRC_germline:
+ tfp->remove_all_germline = TRUE;
+ tfp->move_all_germline = FALSE;
+ break;
+ case SUBSRC_environmental_sample:
+ tfp->remove_all_environmental = TRUE;
+ tfp->move_all_environmental = FALSE;
+ break;
+ case SUBSRC_metagenomic:
+ tfp->remove_all_metagenomic = TRUE;
+ tfp->move_all_metagenomic = FALSE;
+ break;
+ }
+ }
}
else if (fd.move_to_text)
{
- tfp->move_this = TRUE;
- if (fd.do_all)
- {
- switch (subtype)
- {
- case SUBSRC_rearranged:
- tfp->remove_all_rearranged = FALSE;
- tfp->move_all_rearranged = TRUE;
- break;
- case SUBSRC_transgenic:
- tfp->remove_all_transgenic = FALSE;
- tfp->move_all_transgenic = TRUE;
- break;
- case SUBSRC_germline:
- tfp->remove_all_germline = FALSE;
- tfp->move_all_germline = TRUE;
- break;
- case SUBSRC_environmental_sample:
- tfp->remove_all_environmental = FALSE;
- tfp->move_all_environmental = TRUE;
- break;
- case SUBSRC_metagenomic:
- tfp->remove_all_metagenomic = FALSE;
- tfp->move_all_metagenomic = TRUE;
- break;
- }
- }
+ tfp->move_this = TRUE;
+ if (fd.do_all)
+ {
+ switch (subtype)
+ {
+ case SUBSRC_rearranged:
+ tfp->remove_all_rearranged = FALSE;
+ tfp->move_all_rearranged = TRUE;
+ break;
+ case SUBSRC_transgenic:
+ tfp->remove_all_transgenic = FALSE;
+ tfp->move_all_transgenic = TRUE;
+ break;
+ case SUBSRC_germline:
+ tfp->remove_all_germline = FALSE;
+ tfp->move_all_germline = TRUE;
+ break;
+ case SUBSRC_environmental_sample:
+ tfp->remove_all_environmental = FALSE;
+ tfp->move_all_environmental = TRUE;
+ break;
+ case SUBSRC_metagenomic:
+ tfp->remove_all_metagenomic = FALSE;
+ tfp->move_all_metagenomic = TRUE;
+ break;
+ }
+ }
}
}
@@ -2011,76 +2874,76 @@ extern void RemoveTextFromTextFreeSubSourceModifiers (BioSourcePtr biop, Pointer
}
else
{
- tfp = (ModTextFixPtr) userdata;
+ tfp = (ModTextFixPtr) userdata;
}
for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next)
{
- tfp->move_this = FALSE;
- tfp->remove_this = FALSE;
- if ((ssp->subtype == SUBSRC_germline
- || ssp->subtype == SUBSRC_transgenic
- || ssp->subtype == SUBSRC_rearranged
- || ssp->subtype == SUBSRC_environmental_sample
- || ssp->subtype == SUBSRC_metagenomic)
- && ! StringHasNoText (ssp->name))
- {
- GetModifierTextFix (tfp, ssp->subtype, ssp->name);
- if (tfp->move_this)
- {
- /* if a note modifier is found, add this text to it, otherwise create a new
- * note modifier to hold this text.
- */
- if (note_ssp == NULL)
- {
- for (note_ssp = biop->subtype; note_ssp != NULL && note_ssp->subtype != 255; note_ssp = note_ssp->next)
- {
- }
- }
- if (note_ssp == NULL)
- {
- note_ssp = SubSourceNew ();
- if (note_ssp != NULL)
- {
- note_ssp->subtype = 255;
- note_ssp->name = ssp->name;
- ssp->name = StringSave ("");
- note_ssp->next = ssp->next;
- ssp->next = note_ssp;
- }
- }
- else if (StringHasNoText (note_ssp->name))
- {
+ tfp->move_this = FALSE;
+ tfp->remove_this = FALSE;
+ if ((ssp->subtype == SUBSRC_germline
+ || ssp->subtype == SUBSRC_transgenic
+ || ssp->subtype == SUBSRC_rearranged
+ || ssp->subtype == SUBSRC_environmental_sample
+ || ssp->subtype == SUBSRC_metagenomic)
+ && ! StringHasNoText (ssp->name))
+ {
+ GetModifierTextFix (tfp, ssp->subtype, ssp->name);
+ if (tfp->move_this)
+ {
+ /* if a note modifier is found, add this text to it, otherwise create a new
+ * note modifier to hold this text.
+ */
+ if (note_ssp == NULL)
+ {
+ for (note_ssp = biop->subtype; note_ssp != NULL && note_ssp->subtype != 255; note_ssp = note_ssp->next)
+ {
+ }
+ }
+ if (note_ssp == NULL)
+ {
+ note_ssp = SubSourceNew ();
+ if (note_ssp != NULL)
+ {
+ note_ssp->subtype = 255;
+ note_ssp->name = ssp->name;
+ ssp->name = StringSave ("");
+ note_ssp->next = ssp->next;
+ ssp->next = note_ssp;
+ }
+ }
+ else if (StringHasNoText (note_ssp->name))
+ {
note_ssp->name = MemFree (note_ssp->name);
note_ssp->name = ssp->name;
- ssp->name = StringSave ("");
- }
- else
- {
- len = StringLen (note_ssp->name) + StringLen (ssp->name) + 3;
- new_note = (CharPtr) MemNew (len * sizeof (Char));
- if (new_note != NULL)
- {
- StringCpy (new_note, note_ssp->name);
- StringCat (new_note, "; ");
- StringCat (new_note, ssp->name);
- note_ssp->name = MemFree (note_ssp->name);
- note_ssp->name = new_note;
- ssp->name = MemFree (ssp->name);
- ssp->name = StringSave ("");
- }
- }
- }
- else if (tfp->remove_this)
- {
- ssp->name = MemFree (ssp->name);
- ssp->name = StringSave ("");
- }
- }
+ ssp->name = StringSave ("");
+ }
+ else
+ {
+ len = StringLen (note_ssp->name) + StringLen (ssp->name) + 3;
+ new_note = (CharPtr) MemNew (len * sizeof (Char));
+ if (new_note != NULL)
+ {
+ StringCpy (new_note, note_ssp->name);
+ StringCat (new_note, "; ");
+ StringCat (new_note, ssp->name);
+ note_ssp->name = MemFree (note_ssp->name);
+ note_ssp->name = new_note;
+ ssp->name = MemFree (ssp->name);
+ ssp->name = StringSave ("");
+ }
+ }
+ }
+ else if (tfp->remove_this)
+ {
+ ssp->name = MemFree (ssp->name);
+ ssp->name = StringSave ("");
+ }
+ }
}
if (userdata == NULL)
{
- MemFree (tfp);
+ MemFree (tfp);
}
}
@@ -2172,6 +3035,7 @@ Uint2 subsource_types [] = {
TAGLIST_POPUP, TAGLIST_TEXT
};
+/*
static CharPtr orgmod_extra_prompts [] = {
"Additional", "Organism", "Information", NULL
};
@@ -2179,6 +3043,7 @@ static CharPtr orgmod_extra_prompts [] = {
static CharPtr subsource_extra_prompts [] = {
"Additional", "Source", "Information", NULL
};
+*/
static CharPtr orgTabs [] = {
"Names", "Location", "Genetic Codes", "Lineage", NULL
@@ -3429,7 +4294,7 @@ extern Int2 LIBCALLBACK BioSourceGenFunc (Pointer data)
gfp->proctype = ompcp->proc->proctype;
gfp->userkey = OMGetNextUserKey ();
omudp = ObjMgrAddUserData (ompcp->input_entityID, ompcp->proc->procid,
- OMPROC_EDIT, gfp->userkey);
+ OMPROC_EDIT, gfp->userkey);
if (omudp != NULL) {
omudp->userdata.ptrvalue = (Pointer) gfp;
omudp->messagefunc = StdVibrantEditorMsgFunc;
diff --git a/desktop/dlgutil1.c b/desktop/dlgutil1.c
index 6282b598..721a19b5 100644
--- a/desktop/dlgutil1.c
+++ b/desktop/dlgutil1.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 1/22/95
*
-* $Revision: 6.139 $
+* $Revision: 6.141 $
*
* File Description:
*
@@ -1499,7 +1499,7 @@ static void AddProtRefXref (SeqFeatPtr sfp, TexT protXrefName, TexT protXrefDesc
}
}
-static Boolean IsPseudo (SeqFeatPtr sfp)
+static Boolean FeatIsPseudo (SeqFeatPtr sfp)
{
Boolean pseudo = FALSE;
GBQualPtr qual;
@@ -1965,7 +1965,7 @@ extern Boolean FeatFormReplaceWithoutUpdateProc (ForM f)
if (ffp->fidxref != NULL) {
TextToFeatXref (ffp->fidxref, sfp);
}
- if (IsPseudo (sfp))
+ if (FeatIsPseudo (sfp))
{
RemoveProtXrefs (sfp);
}
@@ -5513,8 +5513,11 @@ ReadAlignedSeqLocList
partial5, partial3,
&(loc_list [loc_num])))
{
- loc_list [loc_num] = ValNodeNew (NULL);
- loc_list [loc_num]->choice = SEQLOC_NULL;
+ if (loc_list[loc_num] == NULL)
+ {
+ loc_list [loc_num] = ValNodeNew (NULL);
+ loc_list [loc_num]->choice = SEQLOC_NULL;
+ }
}
}
else
@@ -7399,7 +7402,6 @@ static DialoG LatLonDialog (GrouP h, TaglistCallback change_notify, Pointer chan
static Boolean ParseLatLonOk (CharPtr str)
{
- Boolean rval = FALSE;
CharPtr ns, ew, cp;
if (StringHasNoText (str))
@@ -8809,7 +8811,7 @@ extern void FreeSqnTempFiles (void)
/* This gets a list of the open views */
-NLM_EXTERN ValNodePtr GetBaseFormList ()
+NLM_EXTERN ValNodePtr GetBaseFormList (void)
{
Uint4 j;
diff --git a/desktop/dlgutil2.c b/desktop/dlgutil2.c
index 5380647e..1583a5b6 100644
--- a/desktop/dlgutil2.c
+++ b/desktop/dlgutil2.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 1/22/95
*
-* $Revision: 6.201 $
+* $Revision: 6.203 $
*
* File Description:
*
@@ -4719,7 +4719,8 @@ typedef struct valnodeselection
DIALOG_MESSAGE_BLOCK
DialoG list_dlg;
ValNodePtr choice_list;
-
+
+ Boolean is_multi;
FreeValNodeProc free_vn_proc;
CopyValNodeDataProc copy_vn_proc;
MatchValNodeProc match_vn_proc;
@@ -4747,7 +4748,11 @@ static void ValNodeSelectionListToDialog (DialoG d, Pointer userdata)
for (vnp_list = item_list; vnp_list != NULL; vnp_list = vnp_list->next)
{
found = FALSE;
- for (vnp_sel = dlg->choice_list, i = 1;
+ i = 1;
+ if (dlg->is_multi) {
+ i++;
+ }
+ for (vnp_sel = dlg->choice_list;
vnp_sel != NULL && !found;
vnp_sel = vnp_sel->next, i++)
{
@@ -4924,6 +4929,8 @@ extern DialoG ValNodeSelectionDialogExEx
dlg->match_vn_proc = match_vn_proc;
dlg->remap_vn_proc = remap_vn_proc;
+ dlg->is_multi = allow_multi;
+
for (vnp = choice_list; vnp != NULL; vnp = vnp->next)
{
ValNodeAddPointer (&choice_name_list, 0, (name_proc) (vnp));
@@ -8988,16 +8995,18 @@ static void ClickList (DoC d, PoinT pt)
}
else if (col == cip->level + 2)
{
- cip->expanded = !cip->expanded;
- rsult = GetScrlParams4 (dlg->doc, &offset, &first_shown, NULL);
- PopulateClickableList (dlg, dlg->list_list);
- if (rsult) {
- GetItemParams4 (dlg->doc, first_shown, &offset, NULL, NULL, NULL, NULL);
- SetScrlParams4 (dlg->doc, offset);
+ if (cip->subcategories != NULL) {
+ cip->expanded = !cip->expanded;
+ rsult = GetScrlParams4 (dlg->doc, &offset, &first_shown, NULL);
+ PopulateClickableList (dlg, dlg->list_list);
+ if (rsult) {
+ GetItemParams4 (dlg->doc, first_shown, &offset, NULL, NULL, NULL, NULL);
+ SetScrlParams4 (dlg->doc, offset);
+ }
+ ObjectRect (dlg->doc, &r);
+ InsetRect (&r, -1, -1);
+ InvalRect (&r);
}
- ObjectRect (dlg->doc, &r);
- InsetRect (&r, -1, -1);
- InvalRect (&r);
} else {
dlg->text_select_item_anchor = item;
dlg->text_select_row_anchor = row;
diff --git a/desktop/dlogutil.h b/desktop/dlogutil.h
index 1220a391..fe8336df 100644
--- a/desktop/dlogutil.h
+++ b/desktop/dlogutil.h
@@ -29,7 +29,7 @@
*
* Version Creation Date: 1/22/95
*
-* $Revision: 6.101 $
+* $Revision: 6.102 $
*
* File Description:
*
@@ -765,7 +765,7 @@ extern Boolean FixSpecialCharactersForStringsInList (ValNodePtr find_list, CharP
NLM_EXTERN Boolean FixSpecialCharactersForObject (Uint2 datatype, Pointer objdata, CharPtr msg, Boolean force_fix, BoolPtr changed);
/* for functions that act on all open records */
-NLM_EXTERN ValNodePtr GetBaseFormList ();
+NLM_EXTERN ValNodePtr GetBaseFormList (void);
NLM_EXTERN ValNodePtr GetViewedSeqEntryList (void);
NLM_EXTERN SeqEntryPtr RestoreFromFile (CharPtr path);
NLM_EXTERN Uint2 RestoreEntityIDFromFile (CharPtr path, Uint2 entityID);
diff --git a/desktop/import.c b/desktop/import.c
index f51a33d9..e8776a8a 100644
--- a/desktop/import.c
+++ b/desktop/import.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 6/18/95
*
-* $Revision: 6.70 $
+* $Revision: 6.71 $
*
* File Description:
*
@@ -3505,7 +3505,7 @@ typedef struct visstrpage {
typedef struct visstrform {
DESCRIPTOR_FORM_BLOCK
- Uint2 subtype;
+ Uint1 subtype;
} VisStrForm, PNTR VisStrFormPtr;
static void CharPtrToVisStrPage (DialoG d, Pointer data)
@@ -3647,8 +3647,91 @@ static void VisStrFormMessage (ForM f, Int2 mssg)
}
}
+
+static CharPtr citInCommentMsg =
+"This comment looks like it has citation references in [#] form.\n\
+You should put comments about references in the REMARK section by\n\
+double clicking on the reference and launching its editor.\n\
+Continue saving this comment?";
+
+
+typedef struct replacevisstr {
+ Uint1 subtype;
+ CharPtr deleteThis;
+ CharPtr replaceWith;
+} ReplaceVisStrData, PNTR ReplaceVisStrPtr;
+
+static void ReplaceAllCallback (SeqDescrPtr sdp, Pointer data)
+
+{
+ ReplaceVisStrPtr rp;
+
+ if ((rp = (ReplaceVisStrPtr) data) == NULL || sdp == NULL || sdp->choice != rp->subtype) {
+ return;
+ }
+
+ if (StringCmp (sdp->data.ptrvalue, rp->deleteThis) == 0) {
+ sdp->data.ptrvalue = MemFree (sdp->data.ptrvalue);
+ sdp->data.ptrvalue = StringSave (rp->replaceWith);
+ }
+}
+
+
+static void ReplaceAllVisibleStringsButtonProc (ButtoN b)
+{
+ VisStrFormPtr vfp;
+ Boolean suspicious = FALSE;
+ SeqEntryPtr sep;
+ ReplaceVisStrData rd;
+ SeqDescrPtr sdp_orig;
+ SeqMgrDescContext context;
+
+ vfp = (VisStrFormPtr) GetObjectExtra (b);
+ if (vfp == NULL) {
+ return;
+ }
+
+ rd.subtype = vfp->subtype;
+ rd.replaceWith = DialogToPointer (vfp->data);
+ if (rd.replaceWith == NULL || StringHasNoText (rd.replaceWith)) {
+ Message (MSG_ERROR, "Must supply text!");
+ rd.replaceWith = MemFree (rd.replaceWith);
+ return;
+ }
+
+ sdp_orig = SeqMgrGetDesiredDescriptor (vfp->input_entityID, NULL, vfp->input_itemID, 0, NULL, &context);
+ if (sdp_orig == NULL || sdp_orig->choice != vfp->subtype) {
+ Message (MSG_ERROR, "Unable to find original descriptor!");
+ Remove (vfp->form);
+ rd.replaceWith = MemFree (rd.replaceWith);
+ return;
+ }
+ rd.deleteThis = StringSave (sdp_orig->data.ptrvalue);
+
+ if (vfp->subtype == Seq_descr_comment) {
+ suspicious = SerialNumberInString (rd.replaceWith);
+ }
+ if (suspicious) {
+ if (Message (MSG_OKC, "%s", citInCommentMsg) == ANS_CANCEL) {
+ rd.deleteThis = MemFree (rd.deleteThis);
+ rd.replaceWith = MemFree (rd.replaceWith);
+ return;
+ }
+ }
+
+ sep = GetTopSeqEntryForEntityID (vfp->input_entityID);
+ VisitDescriptorsInSep (sep, &rd, ReplaceAllCallback);
+
+ GetRidOfEmptyFeatsDescStrings (vfp->input_entityID, NULL);
+ ObjMgrSetDirtyFlag (vfp->input_entityID, TRUE);
+ ObjMgrSendMsg (OM_MSG_UPDATE, vfp->input_entityID,
+ vfp->input_itemID, vfp->input_itemtype);
+ Remove (vfp->form);
+}
+
+
extern ForM CreateVisStrForm (Int2 left, Int2 top, CharPtr title,
- Uint2 subtype, FormActnFunc actproc)
+ Uint2 subtype, FormActnFunc actproc, SeqDescrPtr sdp)
{
ButtoN b;
@@ -3666,7 +3749,7 @@ extern ForM CreateVisStrForm (Int2 left, Int2 top, CharPtr title,
vfp->form = (ForM) w;
vfp->actproc = actproc;
vfp->formmessage = VisStrFormMessage;
- vfp->subtype = subtype;
+ vfp->subtype = (Uint1)subtype;
#ifndef WIN_MAC
CreateStdEditorFormMenus (w);
@@ -3681,9 +3764,18 @@ extern ForM CreateVisStrForm (Int2 left, Int2 top, CharPtr title,
g = HiddenGroup (w, -1, 0, NULL);
vfp->data = CreateVisStrDialog (g, NULL, subtype);
- c = HiddenGroup (w, 2, 0, NULL);
- b = PushButton (c, "Accept", StdAcceptFormButtonProc);
- SetObjectExtra (b, vfp, NULL);
+ c = HiddenGroup (w, 3, 0, NULL);
+
+ if (sdp == NULL) {
+ b = PushButton (c, "Accept", StdAcceptFormButtonProc);
+ SetObjectExtra (b, vfp, NULL);
+ } else {
+ b = PushButton (c, "Replace All", ReplaceAllVisibleStringsButtonProc);
+ SetObjectExtra (b, vfp, NULL);
+ b = PushButton (c, "Replace This", StdAcceptFormButtonProc);
+ SetObjectExtra (b, vfp, NULL);
+ }
+
PushButton (c, "Cancel", StdCancelButtonProc);
AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL);
RealizeWindow (w);
@@ -3691,12 +3783,6 @@ extern ForM CreateVisStrForm (Int2 left, Int2 top, CharPtr title,
return (ForM) w;
}
-static CharPtr citInCommentMsg =
-"This comment looks like it has citation references in [#] form.\n\
-You should put comments about references in the REMARK section by\n\
-double clicking on the reference and launching its editor.\n\
-Continue saving this comment?";
-
static void VisStrDescFormActnProc (ForM f)
{
@@ -3798,16 +3884,16 @@ extern Int2 LIBCALLBACK VisStrGenFunc (Pointer data)
}
if (subtype == Seq_descr_title) {
w = (WindoW) CreateVisStrForm (-50, -33, "Title",
- subtype, VisStrDescFormActnProc);
+ subtype, VisStrDescFormActnProc, sdp);
} else if (subtype == Seq_descr_comment) {
w = (WindoW) CreateVisStrForm (-50, -33, "Comment",
- subtype, VisStrDescFormActnProc);
+ subtype, VisStrDescFormActnProc, sdp);
} else if (subtype == Seq_descr_name) {
w = (WindoW) CreateVisStrForm (-50, -33, "Name",
- subtype, VisStrDescFormActnProc);
+ subtype, VisStrDescFormActnProc, sdp);
} else if (subtype == Seq_descr_region) {
w = (WindoW) CreateVisStrForm (-50, -33, "Region",
- subtype, VisStrDescFormActnProc);
+ subtype, VisStrDescFormActnProc, sdp);
} else {
return OM_MSG_RET_ERROR;
}
diff --git a/desktop/import.h b/desktop/import.h
index e656352f..f61fe11a 100644
--- a/desktop/import.h
+++ b/desktop/import.h
@@ -29,7 +29,7 @@
*
* Version Creation Date: 6/18/95
*
-* $Revision: 6.7 $
+* $Revision: 6.8 $
*
* File Description:
*
@@ -111,7 +111,7 @@ extern Int2 LIBCALLBACK GenBankGenFunc (Pointer data);
#define REGISTER_NAME_EDIT ObjMgrProcLoad(OMPROC_EDIT,"Edit Name","Name",OBJ_SEQDESC,Seq_descr_name,OBJ_SEQDESC,Seq_descr_name,NULL,VisStrGenFunc,PROC_PRIORITY_DEFAULT)
extern ForM CreateVisStrForm (Int2 left, Int2 top, CharPtr title,
- Uint2 subtype, FormActnFunc actproc);
+ Uint2 subtype, FormActnFunc actproc, SeqDescrPtr sdp);
extern Int2 LIBCALLBACK VisStrGenFunc (Pointer data);
diff --git a/desktop/macrodlg.c b/desktop/macrodlg.c
index 4a6ca819..2c55a14f 100755
--- a/desktop/macrodlg.c
+++ b/desktop/macrodlg.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 11/23/2007
*
-* $Revision: 1.130 $
+* $Revision: 1.147 $
*
* File Description:
*
@@ -559,6 +559,26 @@ static ConvertFeatureActionPtr BuildDefaultConvertFeatureAction(void)
}
+static RemoveDescriptorActionPtr BuildDefaultRemoveDescriptorAction(void)
+{
+ RemoveDescriptorActionPtr remove;
+
+ remove = RemoveDescriptorActionNew();
+ remove->type = Descriptor_type_all;
+ return remove;
+}
+
+
+static AutodefActionPtr BuildDefaultAutodefAction(void)
+{
+ AutodefActionPtr autodef;
+
+ autodef = AutodefActionNew();
+ autodef->clause_list_type = Autodef_list_type_complete_sequence;
+ return autodef;
+}
+
+
static ValNodePtr BuildDefaultNewMacroAction (void)
{
ValNodePtr vnp;
@@ -2891,7 +2911,7 @@ static void CDSGeneProtPseudoConstraintToDialog (DialoG d, Pointer data)
PointerToDialog (dlg->feat, NULL);
SetValue (dlg->pseudo, 1);
} else {
- vn.choice = pseudo->feature;
+ vn.choice = (Uint1) pseudo->feature;
vn.data.ptrvalue = NULL;
vn.next = NULL;
PointerToDialog (dlg->feat, &vn);
@@ -3580,9 +3600,9 @@ static void SequenceQualPairToDialog (DialoG d, Pointer data)
PointerToDialog (dlg->molecule_from_dlg, NULL);
PointerToDialog (dlg->molecule_to_dlg, NULL);
} else {
- vn.choice = ((MolinfoMoleculePairPtr) m_fields->data.ptrvalue)->from;
+ vn.choice = (Uint1)((MolinfoMoleculePairPtr) m_fields->data.ptrvalue)->from;
PointerToDialog (dlg->molecule_from_dlg, &vn);
- vn.choice = ((MolinfoMoleculePairPtr) m_fields->data.ptrvalue)->to;
+ vn.choice = (Uint1)((MolinfoMoleculePairPtr) m_fields->data.ptrvalue)->to;
PointerToDialog (dlg->molecule_to_dlg, &vn);
}
break;
@@ -3592,9 +3612,9 @@ static void SequenceQualPairToDialog (DialoG d, Pointer data)
PointerToDialog (dlg->technique_from_dlg, NULL);
PointerToDialog (dlg->technique_to_dlg, NULL);
} else {
- vn.choice = ((MolinfoTechniquePairPtr) m_fields->data.ptrvalue)->from;
+ vn.choice = (Uint1)((MolinfoTechniquePairPtr) m_fields->data.ptrvalue)->from;
PointerToDialog (dlg->technique_from_dlg, &vn);
- vn.choice = ((MolinfoTechniquePairPtr) m_fields->data.ptrvalue)->to;
+ vn.choice = (Uint1)((MolinfoTechniquePairPtr) m_fields->data.ptrvalue)->to;
PointerToDialog (dlg->technique_to_dlg, &vn);
}
break;
@@ -3604,9 +3624,9 @@ static void SequenceQualPairToDialog (DialoG d, Pointer data)
PointerToDialog (dlg->completedness_from_dlg, NULL);
PointerToDialog (dlg->completedness_to_dlg, NULL);
} else {
- vn.choice = ((MolinfoCompletednessPairPtr) m_fields->data.ptrvalue)->from;
+ vn.choice = (Uint1)((MolinfoCompletednessPairPtr) m_fields->data.ptrvalue)->from;
PointerToDialog (dlg->completedness_from_dlg, &vn);
- vn.choice = ((MolinfoCompletednessPairPtr) m_fields->data.ptrvalue)->to;
+ vn.choice = (Uint1)((MolinfoCompletednessPairPtr) m_fields->data.ptrvalue)->to;
PointerToDialog (dlg->completedness_to_dlg, &vn);
}
break;
@@ -3616,9 +3636,9 @@ static void SequenceQualPairToDialog (DialoG d, Pointer data)
PointerToDialog (dlg->mol_class_from_dlg, NULL);
PointerToDialog (dlg->mol_class_to_dlg, NULL);
} else {
- vn.choice = ((MolinfoMolClassPairPtr) m_fields->data.ptrvalue)->from;
+ vn.choice = (Uint1)((MolinfoMolClassPairPtr) m_fields->data.ptrvalue)->from;
PointerToDialog (dlg->mol_class_from_dlg, &vn);
- vn.choice = ((MolinfoMolClassPairPtr) m_fields->data.ptrvalue)->to;
+ vn.choice = (Uint1)((MolinfoMolClassPairPtr) m_fields->data.ptrvalue)->to;
PointerToDialog (dlg->mol_class_to_dlg, &vn);
}
break;
@@ -3628,9 +3648,9 @@ static void SequenceQualPairToDialog (DialoG d, Pointer data)
PointerToDialog (dlg->topology_from_dlg, NULL);
PointerToDialog (dlg->topology_to_dlg, NULL);
} else {
- vn.choice = ((MolinfoTopologyPairPtr) m_fields->data.ptrvalue)->from;
+ vn.choice = (Uint1)((MolinfoTopologyPairPtr) m_fields->data.ptrvalue)->from;
PointerToDialog (dlg->topology_from_dlg, &vn);
- vn.choice = ((MolinfoTopologyPairPtr) m_fields->data.ptrvalue)->to;
+ vn.choice = (Uint1)((MolinfoTopologyPairPtr) m_fields->data.ptrvalue)->to;
PointerToDialog (dlg->topology_to_dlg, &vn);
}
break;
@@ -3640,9 +3660,9 @@ static void SequenceQualPairToDialog (DialoG d, Pointer data)
PointerToDialog (dlg->strand_from_dlg, NULL);
PointerToDialog (dlg->strand_to_dlg, NULL);
} else {
- vn.choice = ((MolinfoStrandPairPtr) m_fields->data.ptrvalue)->from;
+ vn.choice = (Uint1)((MolinfoStrandPairPtr) m_fields->data.ptrvalue)->from;
PointerToDialog (dlg->strand_from_dlg, &vn);
- vn.choice = ((MolinfoStrandPairPtr) m_fields->data.ptrvalue)->to;
+ vn.choice = (Uint1)((MolinfoStrandPairPtr) m_fields->data.ptrvalue)->to;
PointerToDialog (dlg->strand_to_dlg, &vn);
}
break;
@@ -4425,7 +4445,7 @@ static void PublicationConstraintToDialog (DialoG d, Pointer data)
PointerToDialog (dlg->field_type, NULL);
PointerToDialog (dlg->string_constraint, NULL);
} else {
- vn.choice = constraint->field->field;
+ vn.choice = (Uint1)constraint->field->field;
vn.data.ptrvalue = NULL;
vn.next = NULL;
PointerToDialog (dlg->field_type, &vn);
@@ -4613,7 +4633,7 @@ static void SequenceConstraintToDialog (DialoG d, Pointer data)
PointerToDialog (dlg->feature_type, NULL);
} else {
SetStatus (dlg->feat_present, TRUE);
- vn.choice = constraint->feature;
+ vn.choice = (Uint1)constraint->feature;
vn.data.ptrvalue = NULL;
vn.next = NULL;
PointerToDialog (dlg->feature_type, &vn);
@@ -6360,7 +6380,7 @@ static void DataToFeatureFieldConstraintDlg (DialoG d, Pointer data)
PointerToDialog (dlg->feature_type, NULL);
PointerToDialog (dlg->feature_field, NULL);
} else {
- vn.choice = ff->type;
+ vn.choice = (Uint1)ff->type;
vn.data.ptrvalue = NULL;
vn.next = NULL;
PointerToDialog (dlg->feature_type, &vn);
@@ -7214,7 +7234,6 @@ static ValNodePtr TestRnaFeatureTypeDialog (DialoG d)
{
RnaFeatureTypeDlgPtr dlg;
ValNodePtr vnp, err_list = NULL;
- CharPtr c;
dlg = (RnaFeatureTypeDlgPtr) GetObjectExtra (d);
if (dlg == NULL) return NULL;
@@ -7222,12 +7241,6 @@ static ValNodePtr TestRnaFeatureTypeDialog (DialoG d)
vnp = DialogToPointer (dlg->rna_type_dlg);
if (vnp == NULL) {
ValNodeAddPointer (&err_list, 0, "no type");
- } else if (vnp->choice == RnaFeatType_ncRNA) {
- c = DialogToPointer (dlg->ncrna_class_dlg);
- if (StringHasNoText (c)) {
- ValNodeAddPointer (&err_list, 0, "no class");
- }
- c = MemFree (c);
}
vnp = ValNodeFree (vnp);
return err_list;
@@ -7300,7 +7313,7 @@ static void RnaQualToDialog (DialoG d, Pointer data)
PointerToDialog (dlg->field_dlg, NULL);
} else {
PointerToDialog (dlg->rnafeat_dlg, q->type);
- vn.choice = q->field;
+ vn.choice = (Uint1)q->field;
vn.data.ptrvalue = NULL;
vn.next = NULL;
PointerToDialog (dlg->field_dlg, &vn);
@@ -7608,7 +7621,7 @@ static void FieldTypeToDialog (DialoG d, Pointer data)
PointerToDialog (dlg->feature_type, NULL);
PointerToDialog (dlg->feature_field, NULL);
} else {
- vn.choice = ffp->type;
+ vn.choice = (Uint1)ffp->type;
vn.data.ptrvalue = NULL;
vn.next = NULL;
PointerToDialog (dlg->feature_type, &vn);
@@ -7865,7 +7878,7 @@ static void FieldPairTypeToDialog (DialoG d, Pointer data)
PointerToDialog (dlg->feature_field_from, NULL);
PointerToDialog (dlg->feature_field_to, NULL);
} else {
- vn.choice = ffp->type;
+ vn.choice = (Uint1)ffp->type;
vn.data.ptrvalue = NULL;
vn.next = NULL;
PointerToDialog (dlg->feature_type, &vn);
@@ -7904,11 +7917,11 @@ static void FieldPairTypeToDialog (DialoG d, Pointer data)
PointerToDialog (dlg->rna_field_to, NULL);
} else {
PointerToDialog (dlg->rna_feat_dlg, rna_quals->type);
- vn.choice = rna_quals->field_from;
+ vn.choice = (Uint1)rna_quals->field_from;
vn.data.ptrvalue = NULL;
vn.next = NULL;
PointerToDialog (dlg->rna_field_from, &vn);
- vn.choice = rna_quals->field_to;
+ vn.choice = (Uint1)rna_quals->field_to;
PointerToDialog (dlg->rna_field_to, &vn);
}
dlg->field_type = FieldPairType_rna_field;
@@ -9617,6 +9630,9 @@ typedef struct applyfeatureactiondlg {
/* for import features */
DialoG quals;
+ /* for source features */
+ DialoG src_quals;
+
/* for all */
TexT gene_locus;
TexT gene_description;
@@ -9811,6 +9827,7 @@ static void ApplyFeatureActionToDialog (DialoG d, Pointer data)
LocationIntervalPtr lint;
CharPtr txt;
ValNode vn;
+ BioSourcePtr biop;
dlg = (ApplyFeatureActionDlgPtr) GetObjectExtra (d);
if (dlg == NULL) {
@@ -9845,6 +9862,9 @@ static void ApplyFeatureActionToDialog (DialoG d, Pointer data)
/* for import features */
PointerToDialog (dlg->quals, NULL);
+
+ /* for source features */
+ PointerToDialog (dlg->src_quals, NULL);
/* for all */
SafeSetTitle (dlg->gene_locus, "");
@@ -9912,6 +9932,11 @@ static void ApplyFeatureActionToDialog (DialoG d, Pointer data)
SafeSetTitle (dlg->protein_name, FindFeatQualValue (action->fields, Feat_qual_legal_product));
SafeSetTitle (dlg->protein_description, FindFeatQualValue (action->fields, Feat_qual_legal_description));
+ /* for source feature */
+ biop = BioSourceFromSourceQualVals (action->src_fields);
+ PointerToDialog (dlg->src_quals, biop);
+ biop = BioSourceFree (biop);
+
/* for RNA */
PointerToDialog (dlg->ncrna_class, FindFeatQualValue (action->fields, Feat_qual_legal_ncRNA_class));
SafeSetTitle (dlg->rna_name, FindFeatQualValue (action->fields, Feat_qual_legal_product));
@@ -9939,6 +9964,7 @@ static Pointer DialogToApplyFeatureAction (DialoG d)
Int4 frame;
GBQualPtr gbq;
ValNodePtr vnp;
+ BioSourcePtr biop;
dlg = (ApplyFeatureActionDlgPtr) GetObjectExtra (d);
if (dlg == NULL) {
@@ -10041,6 +10067,13 @@ static Pointer DialogToApplyFeatureAction (DialoG d)
txt = MemFree (txt);
}
+ /* for source features */
+ if (dlg->src_quals != NULL) {
+ biop = DialogToPointer (dlg->src_quals);
+ action->src_fields = SourceQualValsFromBioSourcePtr (biop);
+ biop = BioSourceFree (biop);
+ }
+
/* for import features */
if (dlg->quals != NULL) {
gbq = DialogToPointer (dlg->quals);
@@ -10150,6 +10183,7 @@ ApplyFeatureActionDialog
ButtoN comment_btn;
ValNodePtr feature_type_list = NULL;
SeqFeatPtr sfp;
+ BioSourcePtr biop;
dlg = (ApplyFeatureActionDlgPtr) MemNew (sizeof (ApplyFeatureActionDlgData));
p = HiddenGroup (h, -1, 0, NULL);
@@ -10248,7 +10282,13 @@ ApplyFeatureActionDialog
PopupItem (dlg->reading_frame, "3");
PopupItem (dlg->reading_frame, "Best");
SetValue (dlg->reading_frame, 4);
- }
+ } else if (action != NULL && action->type == Feature_type_source) {
+ dlg->src_quals = BioSourceDialog (p);
+ biop = BioSourceFromSourceQualVals (action->src_fields);
+ PointerToDialog (dlg->src_quals, biop);
+ biop = BioSourceFree (biop);
+ }
+
r = HiddenGroup (p, 2, 0, NULL);
if (action != NULL && action->type == Feature_type_cds) {
@@ -10273,7 +10313,7 @@ ApplyFeatureActionDialog
StaticPrompt (r, "ncRNA Class", 0, dialogTextHeight, programFont, 'l');
dlg->ncrna_class = CreatencRNAClassDialog (r, FALSE, NULL, NULL);
}
- } else if (action != NULL && action->type != Feature_type_gene) {
+ } else if (action != NULL && action->type != Feature_type_gene && action->type != Feature_type_source) {
StaticPrompt (r, "Qualifiers", 0, dialogTextHeight, programFont, 'l');
sfp = CreateFeatureWithImportFeatureQuals (action);
dlg->quals = NewCreateImportFields (r, GetFeatureNameFromFeatureType (action->type), sfp, FALSE);
@@ -10295,14 +10335,42 @@ ApplyFeatureActionDialog
SetObjectExtra (comment_btn, dlg, NULL);
}
- AlignObjects (ALIGN_CENTER, (HANDLE) dlg->feature_type_dlg,
- (HANDLE) parts_group,
- (HANDLE) g,
- (HANDLE) dlg->strand_group,
- (HANDLE) indexer_only_group,
- (HANDLE) r,
- (HANDLE) (frame_grp != NULL ? frame_grp : comment_btns_grp),
- NULL);
+ if (frame_grp != NULL) {
+ AlignObjects (ALIGN_CENTER, (HANDLE) dlg->feature_type_dlg,
+ (HANDLE) parts_group,
+ (HANDLE) g,
+ (HANDLE) dlg->strand_group,
+ (HANDLE) indexer_only_group,
+ (HANDLE) r,
+ (HANDLE) frame_grp,
+ NULL);
+ } else if (comment_btns_grp != NULL) {
+ AlignObjects (ALIGN_CENTER, (HANDLE) dlg->feature_type_dlg,
+ (HANDLE) parts_group,
+ (HANDLE) g,
+ (HANDLE) dlg->strand_group,
+ (HANDLE) indexer_only_group,
+ (HANDLE) r,
+ (HANDLE) comment_btns_grp,
+ NULL);
+ } else if (dlg->src_quals != NULL) {
+ AlignObjects (ALIGN_CENTER, (HANDLE) dlg->feature_type_dlg,
+ (HANDLE) parts_group,
+ (HANDLE) g,
+ (HANDLE) dlg->strand_group,
+ (HANDLE) indexer_only_group,
+ (HANDLE) r,
+ (HANDLE) dlg->src_quals,
+ NULL);
+ } else {
+ AlignObjects (ALIGN_CENTER, (HANDLE) dlg->feature_type_dlg,
+ (HANDLE) parts_group,
+ (HANDLE) g,
+ (HANDLE) dlg->strand_group,
+ (HANDLE) indexer_only_group,
+ (HANDLE) r,
+ NULL);
+ }
return (DialoG) p;
}
@@ -10331,7 +10399,7 @@ static void RemoveFeatureActionToDialog (DialoG d, Pointer data)
PointerToDialog (dlg->feature_type_dlg, NULL);
PointerToDialog (dlg->constraint_dlg, NULL);
} else {
- vn.choice = action->type;
+ vn.choice = (Uint1)action->type;
vn.data.ptrvalue = NULL;
vn.next = NULL;
PointerToDialog (dlg->feature_type_dlg, &vn);
@@ -10594,9 +10662,9 @@ static void ConvertFeatureActionToDialog (DialoG d, Pointer data)
} else {
vn.next = NULL;
vn.data.ptrvalue = NULL;
- vn.choice = action->type_from;
+ vn.choice = (Uint1)action->type_from;
PointerToDialog (dlg->feature_type_from_dlg, &vn);
- vn.choice = action->type_to;
+ vn.choice = (Uint1)action->type_to;
PointerToDialog (dlg->feature_type_to_dlg, &vn);
/* set source options */
if (action->src_options != NULL && action->src_options->choice == ConvertFeatureSrcOptions_cds) {
@@ -10829,6 +10897,289 @@ static DialoG ConvertFeatureActionDialog
}
+static DialoG DescriptorTypeDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+ ValNodePtr desc_list = NULL;
+
+ AddAllDescriptorsToChoiceList (&desc_list);
+ return ValNodeSelectionDialog (h, desc_list, TALL_SELECTION_LIST, ValNodeStringName,
+ ValNodeSimpleDataFree, ValNodeStringCopy,
+ ValNodeChoiceMatch, "descriptor type",
+ change_notify, change_userdata, FALSE);
+}
+
+
+typedef struct removedescriptoractiondlg {
+ DIALOG_MESSAGE_BLOCK
+ DialoG descriptor_type_dlg;
+
+ DialoG constraint_dlg;
+ Nlm_ChangeNotifyProc change_notify;
+ Pointer change_userdata;
+} RemoveDescriptorActionDlgData, PNTR RemoveDescriptorActionDlgPtr;
+
+
+static void RemoveDescriptorActionToDialog (DialoG d, Pointer data)
+{
+ RemoveDescriptorActionDlgPtr dlg;
+ RemoveDescriptorActionPtr action;
+ ValNode vn;
+
+ dlg = (RemoveDescriptorActionDlgPtr) GetObjectExtra (d);
+ if (dlg == NULL) {
+ return;
+ }
+
+ vn.data.ptrvalue = NULL;
+ vn.next = NULL;
+
+ action = (RemoveDescriptorActionPtr) data;
+ if (action == NULL) {
+ vn.choice = Descriptor_type_all;
+ PointerToDialog (dlg->descriptor_type_dlg, &vn);
+ PointerToDialog (dlg->constraint_dlg, NULL);
+ } else {
+ vn.choice = (Uint1)action->type;
+ PointerToDialog (dlg->descriptor_type_dlg, &vn);
+ PointerToDialog (dlg->constraint_dlg, action->constraint);
+ }
+}
+
+
+static Pointer DialogToRemoveDescriptorAction (DialoG d)
+{
+ RemoveDescriptorActionDlgPtr dlg;
+ RemoveDescriptorActionPtr action;
+ ValNodePtr vnp;
+
+ dlg = (RemoveDescriptorActionDlgPtr) GetObjectExtra (d);
+ if (dlg == NULL) {
+ return NULL;
+ }
+
+ action = RemoveDescriptorActionNew();
+
+ vnp = DialogToPointer (dlg->descriptor_type_dlg);
+ if (vnp == NULL) {
+ action->type = Descriptor_type_all;
+ } else {
+ action->type = vnp->choice;
+ }
+ vnp = ValNodeFree (vnp);
+ action->constraint = DialogToPointer (dlg->constraint_dlg);
+ return action;
+}
+
+
+static ValNodePtr TestRemoveDescriptorActionDialog (DialoG d)
+{
+ RemoveDescriptorActionDlgPtr dlg;
+
+ dlg = (RemoveDescriptorActionDlgPtr) GetObjectExtra (d);
+ if (dlg == NULL) {
+ return NULL;
+ }
+
+ return TestDialog (dlg->descriptor_type_dlg);
+}
+
+
+static DialoG RemoveDescriptorActionDialog
+(GrouP h,
+ Boolean indexer_version,
+ Nlm_ChangeNotifyProc change_notify,
+ Pointer change_userdata)
+{
+ RemoveDescriptorActionDlgPtr dlg;
+ GrouP p;
+
+ dlg = (RemoveDescriptorActionDlgPtr) MemNew (sizeof (RemoveDescriptorActionDlgData));
+ p = HiddenGroup (h, -1, 0, NULL);
+ SetGroupSpacing (p, 10, 10);
+ SetObjectExtra (p, dlg, StdCleanupExtraProc);
+
+ dlg->dialog = (DialoG) p;
+ dlg->todialog = RemoveDescriptorActionToDialog;
+ dlg->fromdialog = DialogToRemoveDescriptorAction;
+ dlg->dialogmessage = NULL;
+ dlg->testdialog = TestRemoveDescriptorActionDialog;
+ dlg->change_notify = change_notify;
+ dlg->change_userdata = change_userdata;
+
+ dlg->descriptor_type_dlg = DescriptorTypeDialog (p, change_notify, change_userdata);
+
+ dlg->constraint_dlg = ConstraintSetDialog (p, change_notify, change_userdata);
+
+ AlignObjects (ALIGN_CENTER, (HANDLE) dlg->descriptor_type_dlg, (HANDLE) dlg->constraint_dlg, NULL);
+
+ return (DialoG) p;
+}
+
+
+typedef struct autodefactiondlg {
+ DIALOG_MESSAGE_BLOCK
+ DialoG modifiers_dlg;
+ PopuP clause_list_type_popup;
+
+ Nlm_ChangeNotifyProc change_notify;
+ Pointer change_userdata;
+} AutodefActionDlgData, PNTR AutodefActionDlgPtr;
+
+
+static void AutodefActionToDialog(DialoG d, Pointer data)
+{
+ AutodefActionDlgPtr dlg;
+ AutodefActionPtr action;
+ ValNodePtr list = NULL, vnp;
+
+ dlg = (AutodefActionDlgPtr) GetObjectExtra (d);
+ if (dlg == NULL) {
+ return;
+ }
+ action = (AutodefActionPtr) data;
+ if (action == NULL) {
+ PointerToDialog (dlg->modifiers_dlg, NULL);
+ SetValue (dlg->clause_list_type_popup, 2);
+ } else {
+ /* populate modifiers */
+ for (vnp = action->modifiers; vnp != NULL; vnp = vnp->next) {
+ ValNodeAddPointer (&list, 0, GetSourceQualName (vnp->data.intvalue));
+ }
+ PointerToDialog (dlg->modifiers_dlg, list);
+
+ /* populate clause list type */
+ switch (action->clause_list_type) {
+ case Autodef_list_type_feature_list:
+ SetValue (dlg->clause_list_type_popup, 1);
+ break;
+ case Autodef_list_type_complete_sequence:
+ SetValue (dlg->clause_list_type_popup, 2);
+ break;
+ case Autodef_list_type_complete_genome:
+ SetValue (dlg->clause_list_type_popup, 3);
+ break;
+ default:
+ SetValue (dlg->clause_list_type_popup, 2);
+ break;
+ }
+ }
+}
+
+
+static Pointer DialogToAutodefAction (DialoG d)
+{
+ AutodefActionDlgPtr dlg;
+ AutodefActionPtr action = NULL;
+ Int2 v;
+ ValNodePtr list, vnp;
+
+ dlg = (AutodefActionDlgPtr) GetObjectExtra (d);
+ if (dlg == NULL) {
+ return NULL;
+ }
+
+ action = AutodefActionNew();
+ v = GetValue (dlg->clause_list_type_popup);
+ switch (v) {
+ case 1:
+ action->clause_list_type = Autodef_list_type_feature_list;
+ break;
+ case 2:
+ action->clause_list_type = Autodef_list_type_complete_sequence;
+ break;
+ case 3:
+ action->clause_list_type = Autodef_list_type_complete_genome;
+ break;
+ default:
+ action->clause_list_type = Autodef_list_type_feature_list;
+ break;
+ }
+
+ list = DialogToPointer (dlg->modifiers_dlg);
+ for (vnp = list; vnp != NULL; vnp = vnp->next) {
+ ValNodeAddInt (&(action->modifiers), SourceQualChoice_textqual, GetSourceQualTypeByName (vnp->data.ptrvalue));
+ }
+ list = ValNodeFree (list);
+
+ return action;
+}
+
+
+static void ChangeAutodefPopup (PopuP p)
+{
+ AutodefActionDlgPtr dlg;
+
+ dlg = (AutodefActionDlgPtr) GetObjectExtra (p);
+ if (dlg == NULL) {
+ return;
+ }
+ if (dlg->change_notify != NULL) {
+ (dlg->change_notify) (dlg->change_userdata);
+ }
+}
+
+
+static DialoG AutodefActionDialog
+(GrouP h,
+ Boolean indexer_version,
+ Nlm_ChangeNotifyProc change_notify,
+ Pointer change_userdata)
+{
+ AutodefActionDlgPtr dlg;
+ GrouP p;
+ PrompT ppt1, ppt2;
+ ValNodePtr src_quals = NULL;
+ ValNode vn;
+
+ dlg = (AutodefActionDlgPtr) MemNew (sizeof (AutodefActionDlgData));
+ p = HiddenGroup (h, -1, 0, NULL);
+ SetGroupSpacing (p, 10, 10);
+ SetObjectExtra (p, dlg, StdCleanupExtraProc);
+
+ dlg->dialog = (DialoG) p;
+ dlg->todialog = AutodefActionToDialog;
+ dlg->fromdialog = DialogToAutodefAction;
+ dlg->dialogmessage = NULL;
+ dlg->testdialog = NULL;
+ dlg->change_notify = change_notify;
+ dlg->change_userdata = change_userdata;
+
+ ppt1 = StaticPrompt (p, "Modifiers", 0, dialogTextHeight, systemFont, 'l');
+
+ ValNodeAddPointer (&src_quals, 0, StringSave ("clone"));
+ ValNodeAddPointer (&src_quals, 0, StringSave ("cultivar"));
+ ValNodeAddPointer (&src_quals, 0, StringSave ("haplogroup"));
+ ValNodeAddPointer (&src_quals, 0, StringSave ("isolate"));
+ ValNodeAddPointer (&src_quals, 0, StringSave ("strain"));
+ ValNodeAddPointer (&src_quals, 0, StringSave ("specimen-voucher"));
+
+ dlg->modifiers_dlg = ValNodeSelectionDialog (p, src_quals, SHORT_SELECTION_LIST,
+ ValNodeStringName,
+ ValNodeSimpleDataFree,
+ ValNodeStringCopy,
+ ValNodeStringMatch,
+ "source qual",
+ change_notify, change_userdata, TRUE);
+ vn.choice = 0;
+ vn.next = NULL;
+ vn.data.ptrvalue = "haplogroup";
+ PointerToDialog (dlg->modifiers_dlg, &vn);
+
+ ppt2 = StaticPrompt (p, "Features or Complete", 0, dialogTextHeight, systemFont, 'l');
+
+ dlg->clause_list_type_popup = PopupList (p, TRUE, ChangeAutodefPopup);
+ SetObjectExtra (dlg->clause_list_type_popup, dlg, NULL);
+ PopupItem (dlg->clause_list_type_popup, "List Features");
+ PopupItem (dlg->clause_list_type_popup, "Complete Sequence");
+ PopupItem (dlg->clause_list_type_popup, "Complete Genome");
+ SetValue (dlg->clause_list_type_popup, 2);
+
+ AlignObjects (ALIGN_CENTER, (HANDLE) ppt1, (HANDLE) dlg->modifiers_dlg, (HANDLE) ppt2, (HANDLE) dlg->clause_list_type_popup, NULL);
+
+ return (DialoG) p;
+}
+
+
typedef struct editfeaturelocationactiondlg {
DIALOG_MESSAGE_BLOCK
DialoG feature_type_dlg;
@@ -10921,7 +11272,7 @@ static void EditFeatureLocationActionToDialog (DialoG d, Pointer data)
ResetFeatureLocationActionEditType (dlg);
PointerToDialog (dlg->constraint_dlg, NULL);
} else {
- vn.choice = action->type;
+ vn.choice = (Uint1)action->type;
vn.data.ptrvalue = NULL;
vn.next = NULL;
PointerToDialog (dlg->feature_type_dlg, &vn);
@@ -11469,11 +11820,11 @@ static void ChangeParseSrcDialogPopup (PopuP p)
val = GetValue (dlg->main_choice);
switch (val) {
- case 4:
+ case 5:
Show (dlg->src_grp);
Hide (dlg->structured_comment_field);
break;
- case 7:
+ case 8:
Show (dlg->structured_comment_field);
Hide (dlg->src_grp);
break;
@@ -11531,9 +11882,9 @@ static void ParseSrcToDialog (DialoG d, Pointer data)
SetValue (dlg->main_choice, 3);
break;
case ParseSrc_org:
- SetValue (dlg->main_choice, 4);
org = (ParseSrcOrgPtr) src->data.ptrvalue;
if (org == NULL) {
+ SetValue (dlg->main_choice, 5);
SetValue (dlg->feat_or_desc, 1);
PointerToDialog (dlg->src_qual_choice, NULL);
} else {
@@ -11552,34 +11903,38 @@ static void ParseSrcToDialog (DialoG d, Pointer data)
break;
}
if (org->field == NULL) {
- PointerToDialog (dlg->src_qual_choice, NULL);
+ PointerToDialog (dlg->src_qual_choice, NULL);
+ SetValue (dlg->main_choice, 5);
} else if (org->field->choice == ParseSrcOrgChoice_taxname_after_binomial) {
- vn.choice = 0;
- vn.data.ptrvalue = kTaxnameAfterBinomialString;
- vn.next = NULL;
- PointerToDialog (dlg->src_qual_choice, &vn);
+ SetValue (dlg->main_choice, 9);
} else if (org->field->choice == ParseSrcOrgChoice_source_qual) {
vn.choice = 0;
vn.data.ptrvalue = GetSourceQualName (org->field->data.intvalue);
vn.next = NULL;
PointerToDialog (dlg->src_qual_choice, &vn);
+ if (org->field->data.intvalue == Source_qual_taxname) {
+ SetValue (dlg->main_choice, 4);
+ } else {
+ SetValue (dlg->main_choice, 5);
+ }
} else {
PointerToDialog (dlg->src_qual_choice, NULL);
+ SetValue (dlg->main_choice, 5);
}
}
break;
case ParseSrc_comment:
- SetValue (dlg->main_choice, 5);
+ SetValue (dlg->main_choice, 6);
break;
case ParseSrc_bankit_comment:
- SetValue (dlg->main_choice, 6);
+ SetValue (dlg->main_choice, 7);
break;
case ParseSrc_structured_comment:
- SetValue (dlg->main_choice, 7);
+ SetValue (dlg->main_choice, 8);
SetTitle (dlg->structured_comment_field, src->data.ptrvalue);
break;
case ParseSrc_file_id:
- SetValue (dlg->main_choice, 8);
+ SetValue (dlg->main_choice, 10);
break;
default:
SetValue (dlg->main_choice, 0);
@@ -11631,6 +11986,29 @@ static Pointer DialogToParseSrc (DialoG d)
org->type = Object_type_constraint_any;
break;
}
+ org->field = ValNodeNew (NULL);
+ org->field->choice = ParseSrcOrgChoice_source_qual;
+ org->field->data.intvalue = Source_qual_taxname;
+ src = ValNodeNew (NULL);
+ src->choice = ParseSrc_org;
+ src->data.ptrvalue = org;
+ break;
+ case 5:
+ org = ParseSrcOrgNew ();
+ switch (GetValue (dlg->feat_or_desc)) {
+ case 1:
+ org->type = Object_type_constraint_any;
+ break;
+ case 2:
+ org->type = Object_type_constraint_feature;
+ break;
+ case 3:
+ org->type = Object_type_constraint_descriptor;
+ break;
+ default:
+ org->type = Object_type_constraint_any;
+ break;
+ }
vnp = (ValNodePtr) DialogToPointer (dlg->src_qual_choice);
if (vnp != NULL) {
org->field = ValNodeNew (NULL);
@@ -11646,20 +12024,42 @@ static Pointer DialogToParseSrc (DialoG d)
src->choice = ParseSrc_org;
src->data.ptrvalue = org;
break;
- case 5:
+ case 6:
src = ValNodeNew (NULL);
src->choice = ParseSrc_comment;
break;
- case 6:
+ case 7:
src = ValNodeNew (NULL);
src->choice = ParseSrc_bankit_comment;
break;
- case 7:
+ case 8:
src = ValNodeNew (NULL);
src->choice = ParseSrc_structured_comment;
src->data.ptrvalue = SaveStringFromText (dlg->structured_comment_field);
break;
- case 8:
+ case 9:
+ org = ParseSrcOrgNew ();
+ switch (GetValue (dlg->feat_or_desc)) {
+ case 1:
+ org->type = Object_type_constraint_any;
+ break;
+ case 2:
+ org->type = Object_type_constraint_feature;
+ break;
+ case 3:
+ org->type = Object_type_constraint_descriptor;
+ break;
+ default:
+ org->type = Object_type_constraint_any;
+ break;
+ }
+ org->field = ValNodeNew (NULL);
+ org->field->choice = ParseSrcOrgChoice_taxname_after_binomial;
+ src = ValNodeNew (NULL);
+ src->choice = ParseSrc_org;
+ src->data.ptrvalue = org;
+ break;
+ case 10:
src = ValNodeNew (NULL);
src->choice = ParseSrc_file_id;
break;
@@ -11678,11 +12078,11 @@ static ValNodePtr TestParseSrcDialog (DialoG d)
if (dlg == NULL) return NULL;
val = GetValue (dlg->main_choice);
- if (val < 1 || val > 8) {
+ if (val < 1 || val > 10) {
ValNodeAddPointer (&err_list, 0, "main choice");
- } else if (val == 4) {
+ } else if (val == 5) {
ValNodeLink (&err_list, TestDialog (dlg->src_qual_choice));
- } else if (val == 7 && TextHasNoText (dlg->structured_comment_field)) {
+ } else if (val == 8 && TextHasNoText (dlg->structured_comment_field)) {
ValNodeAddPointer (&err_list, 0, "structured comment field");
}
return err_list;
@@ -11711,13 +12111,15 @@ static DialoG ParseSrcDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Point
dlg->main_choice = PopupList (p, TRUE, ChangeParseSrcDialogPopup);
SetObjectExtra (dlg->main_choice, dlg, NULL);
- PopupItem (dlg->main_choice, "Defline");
- PopupItem (dlg->main_choice, "FlatFile");
+ PopupItem (dlg->main_choice, "Definition Line");
+ PopupItem (dlg->main_choice, "GenBank FlatFile");
PopupItem (dlg->main_choice, "Local ID");
+ PopupItem (dlg->main_choice, "Organism Name");
PopupItem (dlg->main_choice, "Source Qualifier");
PopupItem (dlg->main_choice, "Comment");
PopupItem (dlg->main_choice, "BankIT Comment");
PopupItem (dlg->main_choice, "Structured Comment");
+ PopupItem (dlg->main_choice, "Taxname after Binomial");
PopupItem (dlg->main_choice, "File ID");
SetValue (dlg->main_choice, 4);
@@ -11744,6 +12146,7 @@ static DialoG ParseSrcDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Point
RadioButton (dlg->feat_or_desc, "Features Only");
SetValue (dlg->feat_or_desc, 1);
AlignObjects (ALIGN_CENTER, (HANDLE) dlg->src_qual_choice, (HANDLE) dlg->feat_or_desc, NULL);
+ Hide (dlg->src_grp);
dlg->structured_comment_field = DialogText (g, "", 20, ChangeParseSrcDialogText);
SetObjectExtra (dlg->structured_comment_field, dlg, NULL);
@@ -11759,16 +12162,36 @@ typedef struct parsedstdlg {
DIALOG_MESSAGE_BLOCK
PopuP main_choice;
GrouP src_grp;
+ PopuP biosrc_list;
DialoG src_qual_choice;
GrouP feat_or_desc;
+ PopuP gene_field;
+ DialoG rna_field;
+ PopuP protein_field;
GrouP feature_field_grp;
DialoG feature_type_choice;
DialoG feature_field_choice;
+ DialoG feature_note;
TexT dbxref_db;
Nlm_ChangeNotifyProc change_notify;
Pointer change_userdata;
} ParseDstDlgData, PNTR ParseDstDlgPtr;
+typedef enum {
+ eParseDstDialog_defline = 1,
+ eParseDstDialog_biosrc,
+ eParseDstDialog_srcqual,
+ eParseDstDialog_genefield,
+ eParseDstDialog_rnafield,
+ eParseDstDialog_cdscomment,
+ eParseDstDialog_proteinfield,
+ eParseDstDialog_featqual,
+ eParseDstDialog_featnote,
+ eParseDstDialog_commentdesc,
+ eParseDstDialog_dbxref
+} EParseDstDialog;
+
+#define eParseDstDialog_last eParseDstDialog_dbxref
static void ChangeParseDstDialogPopup (PopuP p)
{
@@ -11780,25 +12203,90 @@ static void ChangeParseDstDialogPopup (PopuP p)
val = GetValue (dlg->main_choice);
switch (val) {
- case 2:
+ case eParseDstDialog_biosrc:
Show (dlg->src_grp);
+ Show (dlg->biosrc_list);
+ Hide (dlg->src_qual_choice);
Hide (dlg->feature_field_grp);
Hide (dlg->dbxref_db);
+ Hide (dlg->rna_field);
+ Hide (dlg->gene_field);
+ Hide (dlg->protein_field);
+ Hide (dlg->feature_note);
break;
- case 3:
+ case eParseDstDialog_srcqual:
+ Show (dlg->src_grp);
+ Hide (dlg->biosrc_list);
+ Show (dlg->src_qual_choice);
+ Hide (dlg->feature_field_grp);
+ Hide (dlg->dbxref_db);
+ Hide (dlg->rna_field);
+ Hide (dlg->gene_field);
+ Hide (dlg->protein_field);
+ Hide (dlg->feature_note);
+ break;
+ case eParseDstDialog_genefield:
+ Show (dlg->gene_field);
+ Hide (dlg->src_grp);
+ Hide (dlg->feature_field_grp);
+ Hide (dlg->dbxref_db);
+ Hide (dlg->rna_field);
+ Hide (dlg->protein_field);
+ Hide (dlg->feature_note);
+ break;
+ case eParseDstDialog_rnafield:
+ Show (dlg->rna_field);
+ Hide (dlg->src_grp);
+ Hide (dlg->feature_field_grp);
+ Hide (dlg->dbxref_db);
+ Hide (dlg->gene_field);
+ Hide (dlg->protein_field);
+ Hide (dlg->feature_note);
+ break;
+ case eParseDstDialog_proteinfield:
+ Show (dlg->protein_field);
+ Hide (dlg->rna_field);
+ Hide (dlg->src_grp);
+ Hide (dlg->feature_field_grp);
+ Hide (dlg->dbxref_db);
+ Hide (dlg->gene_field);
+ Hide (dlg->feature_note);
+ break;
+ case eParseDstDialog_featqual:
Hide (dlg->src_grp);
Show (dlg->feature_field_grp);
Hide (dlg->dbxref_db);
+ Hide (dlg->rna_field);
+ Hide (dlg->gene_field);
+ Hide (dlg->protein_field);
+ Hide (dlg->feature_note);
break;
- case 4:
+ case eParseDstDialog_featnote:
+ Show (dlg->feature_note);
+ Hide (dlg->src_grp);
+ Hide (dlg->feature_field_grp);
+ Hide (dlg->dbxref_db);
+ Hide (dlg->rna_field);
+ Hide (dlg->gene_field);
+ Hide (dlg->protein_field);
+ break;
+ case eParseDstDialog_dbxref:
Hide (dlg->src_grp);
Hide (dlg->feature_field_grp);
Show (dlg->dbxref_db);
+ Hide (dlg->rna_field);
+ Hide (dlg->gene_field);
+ Hide (dlg->protein_field);
+ Hide (dlg->feature_note);
break;
default:
Hide (dlg->src_grp);
Hide (dlg->feature_field_grp);
Hide (dlg->dbxref_db);
+ Hide (dlg->rna_field);
+ Hide (dlg->gene_field);
+ Hide (dlg->protein_field);
+ Hide (dlg->feature_note);
break;
}
if (dlg->change_notify != NULL) {
@@ -11833,16 +12321,16 @@ static void ParseDstToDialog (DialoG d, Pointer data)
dst = (ValNodePtr) data;
if (dst == NULL) {
- SetValue (dlg->main_choice, 1);
+ SetValue (dlg->main_choice, eParseDstDialog_defline);
} else {
switch (dst->choice) {
case ParseDest_defline:
- SetValue (dlg->main_choice, 1);
+ SetValue (dlg->main_choice, eParseDstDialog_defline );
break;
case ParseDest_org:
- SetValue (dlg->main_choice, 2);
org = (ParseDstOrgPtr) dst->data.ptrvalue;
if (org == NULL) {
+ SetValue (dlg->main_choice, eParseDstDialog_srcqual);
PointerToDialog (dlg->src_qual_choice, NULL);
SetValue (dlg->feat_or_desc, 1);
} else {
@@ -11862,31 +12350,53 @@ static void ParseDstToDialog (DialoG d, Pointer data)
}
if (org->field == NULL) {
PointerToDialog (dlg->src_qual_choice, NULL);
+ SetValue (dlg->main_choice, eParseDstDialog_srcqual);
} else {
- vn.choice = 0;
- vn.data.ptrvalue = GetSourceQualName (org->field->data.intvalue);
- vn.next = NULL;
- PointerToDialog (dlg->src_qual_choice, &vn);
+ switch (org->field->data.intvalue) {
+ case Source_qual_taxname:
+ SetValue (dlg->biosrc_list, 1);
+ SetValue (dlg->main_choice, eParseDstDialog_biosrc);
+ break;
+ case Source_qual_lineage:
+ SetValue (dlg->biosrc_list, 2);
+ SetValue (dlg->main_choice, eParseDstDialog_biosrc);
+ break;
+ case Source_qual_division:
+ SetValue (dlg->biosrc_list, 3);
+ SetValue (dlg->main_choice, eParseDstDialog_biosrc);
+ break;
+ default:
+ vn.choice = 0;
+ vn.data.ptrvalue = GetSourceQualName (org->field->data.intvalue);
+ vn.next = NULL;
+ PointerToDialog (dlg->src_qual_choice, &vn);
+ SetValue (dlg->main_choice, eParseDstDialog_biosrc);
+ break;
+ }
}
}
break;
case ParseDest_featqual:
- SetValue (dlg->main_choice, 3);
+ /* TODO - look for RNA fields, gene fields, cds comment, feature note? */
+ SetValue (dlg->main_choice, eParseDstDialog_featqual);
ffp = (FeatureFieldLegalPtr) dst->data.ptrvalue;
if (ffp == NULL) {
PointerToDialog (dlg->feature_type_choice, NULL);
PointerToDialog (dlg->feature_field_choice, NULL);
} else {
- vn.choice = ffp->type;
+ vn.choice = (Uint1)ffp->type;
vn.data.ptrvalue = NULL;
vn.next = NULL;
PointerToDialog (dlg->feature_type_choice, &vn);
- vn.choice = ffp->field;
+ vn.choice = (Uint1)ffp->field;
PointerToDialog (dlg->feature_field_choice, &vn);
}
break;
+ case ParseDest_comment_descriptor:
+ SetValue (dlg->main_choice, eParseDstDialog_commentdesc);
+ break;
case ParseDest_dbxref:
- SetValue (dlg->main_choice, 4);
+ SetValue (dlg->main_choice, eParseDstDialog_dbxref);
SetTitle (dlg->dbxref_db, dst->data.ptrvalue);
break;
}
@@ -11901,19 +12411,59 @@ static Pointer DialogToParseDst (DialoG d)
ParseDstDlgPtr dlg;
ParseDstOrgPtr org;
FeatureFieldLegalPtr ffp;
+ FeatureFieldPtr ff;
ValNodePtr dst = NULL, vnp;
- Int2 val;
+ Int2 val, subval;
+ RnaQualPtr rq;
dlg = (ParseDstDlgPtr) GetObjectExtra (d);
if (dlg == NULL) return NULL;
val = GetValue (dlg->main_choice);
switch (val) {
- case 1:
+ case eParseDstDialog_defline:
dst = ValNodeNew (NULL);
dst->choice = ParseDest_defline;
break;
- case 2:
+ case eParseDstDialog_biosrc:
+ org = ParseDstOrgNew ();
+ switch (GetValue (dlg->feat_or_desc)) {
+ case 1:
+ org->type = Object_type_constraint_any;
+ break;
+ case 2:
+ org->type = Object_type_constraint_feature;
+ break;
+ case 3:
+ org->type = Object_type_constraint_descriptor;
+ break;
+ default:
+ org->type = Object_type_constraint_any;
+ break;
+ }
+ subval = GetValue (dlg->biosrc_list);
+ switch (subval) {
+ case 1:
+ org->field = ValNodeNew (NULL);
+ org->field->choice = SourceQualChoice_textqual;
+ org->field->data.intvalue = Source_qual_taxname;
+ break;
+ case 2:
+ org->field = ValNodeNew (NULL);
+ org->field->choice = SourceQualChoice_textqual;
+ org->field->data.intvalue = Source_qual_lineage;
+ break;
+ case 3:
+ org->field = ValNodeNew (NULL);
+ org->field->choice = SourceQualChoice_textqual;
+ org->field->data.intvalue = Source_qual_division;
+ break;
+ }
+ dst = ValNodeNew (NULL);
+ dst->choice = ParseDest_org;
+ dst->data.ptrvalue = org;
+ break;
+ case eParseDstDialog_srcqual:
org = ParseDstOrgNew ();
switch (GetValue (dlg->feat_or_desc)) {
case 1:
@@ -11940,7 +12490,170 @@ static Pointer DialogToParseDst (DialoG d)
dst->choice = ParseDest_org;
dst->data.ptrvalue = org;
break;
- case 3:
+ case eParseDstDialog_genefield:
+ subval = GetValue (dlg->gene_field);
+ switch (subval) {
+ case 1: /* locus */
+ ffp = FeatureFieldLegalNew ();
+ ffp->type = Feature_type_gene;
+ ffp->field = Feat_qual_legal_gene;
+ dst = ValNodeNew (NULL);
+ dst->choice = ParseDest_featqual;
+ dst->data.ptrvalue = ffp;
+ break;
+ case 2: /* description */
+ ffp = FeatureFieldLegalNew ();
+ ffp->type = Feature_type_gene;
+ ffp->field = Feat_qual_legal_gene_description;
+ dst = ValNodeNew (NULL);
+ dst->choice = ParseDest_featqual;
+ dst->data.ptrvalue = ffp;
+ break;
+ case 3: /* comment */
+ ffp = FeatureFieldLegalNew ();
+ ffp->type = Feature_type_gene;
+ ffp->field = Feat_qual_legal_note;
+ dst = ValNodeNew (NULL);
+ dst->choice = ParseDest_featqual;
+ dst->data.ptrvalue = ffp;
+ break;
+ case 4: /* allele */
+ ffp = FeatureFieldLegalNew ();
+ ffp->type = Feature_type_gene;
+ ffp->field = Feat_qual_legal_allele;
+ dst = ValNodeNew (NULL);
+ dst->choice = ParseDest_featqual;
+ dst->data.ptrvalue = ffp;
+ break;
+ case 5: /* maploc */
+ ffp = FeatureFieldLegalNew ();
+ ffp->type = Feature_type_gene;
+ ffp->field = Feat_qual_legal_map;
+ dst = ValNodeNew (NULL);
+ dst->choice = ParseDest_featqual;
+ dst->data.ptrvalue = ffp;
+ break;
+ case 6: /* locus tag */
+ ffp = FeatureFieldLegalNew ();
+ ffp->type = Feature_type_gene;
+ ffp->field = Feat_qual_legal_locus_tag;
+ dst = ValNodeNew (NULL);
+ dst->choice = ParseDest_featqual;
+ dst->data.ptrvalue = ffp;
+ break;
+ case 7: /* synonym */
+ ffp = FeatureFieldLegalNew ();
+ ffp->type = Feature_type_gene;
+ ffp->field = Feat_qual_legal_synonym;
+ dst = ValNodeNew (NULL);
+ dst->choice = ParseDest_featqual;
+ dst->data.ptrvalue = ffp;
+ break;
+ case 8: /* old locus tag */
+ ffp = FeatureFieldLegalNew ();
+ ffp->type = Feature_type_gene;
+ ffp->field = Feat_qual_legal_old_locus_tag;
+ dst = ValNodeNew (NULL);
+ dst->choice = ParseDest_featqual;
+ dst->data.ptrvalue = ffp;
+ break;
+ }
+ break;
+ case eParseDstDialog_rnafield:
+ /* get rna qual, translate to feature qual */
+ rq = DialogToPointer (dlg->rna_field);
+ ff = FeatureFieldFromRnaQual (rq);
+ rq = RnaQualFree (rq);
+ if (ff != NULL) {
+ ffp = FeatureFieldLegalNew ();
+ ffp->type = ff->type;
+ if (ff->field != NULL) {
+ ffp->field = ff->field->data.intvalue;
+ }
+ dst = ValNodeNew (NULL);
+ dst->choice = ParseDest_featqual;
+ dst->data.ptrvalue = ffp;
+ }
+ ff = FeatureFieldFree (ff);
+ break;
+ case eParseDstDialog_cdscomment:
+ ffp = FeatureFieldLegalNew ();
+ ffp->type = Feature_type_cds;
+ ffp->field = Feat_qual_legal_note;
+ dst = ValNodeNew (NULL);
+ dst->choice = ParseDest_featqual;
+ dst->data.ptrvalue = ffp;
+ break;
+ case eParseDstDialog_proteinfield:
+ subval = GetValue (dlg->protein_field);
+ switch (subval) {
+ case 1: /* name */
+ ffp = FeatureFieldLegalNew ();
+ ffp->type = Feature_type_cds;
+ ffp->field = Feat_qual_legal_product;
+ dst = ValNodeNew (NULL);
+ dst->choice = ParseDest_featqual;
+ dst->data.ptrvalue = ffp;
+ break;
+ case 2: /* description */
+ ffp = FeatureFieldLegalNew ();
+ ffp->type = Feature_type_prot;
+ ffp->field = Feat_qual_legal_description;
+ dst = ValNodeNew (NULL);
+ dst->choice = ParseDest_featqual;
+ dst->data.ptrvalue = ffp;
+ break;
+ case 3: /* e.c. number */
+ ffp = FeatureFieldLegalNew ();
+ ffp->type = Feature_type_prot;
+ ffp->field = Feat_qual_legal_ec_number;
+ dst = ValNodeNew (NULL);
+ dst->choice = ParseDest_featqual;
+ dst->data.ptrvalue = ffp;
+ break;
+ case 4: /* activity */
+ ffp = FeatureFieldLegalNew ();
+ ffp->type = Feature_type_prot;
+ ffp->field = Feat_qual_legal_activity;
+ dst = ValNodeNew (NULL);
+ dst->choice = ParseDest_featqual;
+ dst->data.ptrvalue = ffp;
+ break;
+ case 5: /* comment */
+ ffp = FeatureFieldLegalNew ();
+ ffp->type = Feature_type_prot;
+ ffp->field = Feat_qual_legal_note;
+ dst = ValNodeNew (NULL);
+ dst->choice = ParseDest_featqual;
+ dst->data.ptrvalue = ffp;
+ break;
+ case 6: /* mat-peptide name */
+ ffp = FeatureFieldLegalNew ();
+ ffp->type = Feature_type_mat_peptide_aa;
+ ffp->field = Feat_qual_legal_product;
+ dst = ValNodeNew (NULL);
+ dst->choice = ParseDest_featqual;
+ dst->data.ptrvalue = ffp;
+ break;
+ case 7: /* mat-peptide description */
+ ffp = FeatureFieldLegalNew ();
+ ffp->type = Feature_type_mat_peptide_aa;
+ ffp->field = Feat_qual_legal_description;
+ dst = ValNodeNew (NULL);
+ dst->choice = ParseDest_featqual;
+ dst->data.ptrvalue = ffp;
+ break;
+ case 8: /* mat-peptide comment */
+ ffp = FeatureFieldLegalNew ();
+ ffp->type = Feature_type_mat_peptide_aa;
+ ffp->field = Feat_qual_legal_note;
+ dst = ValNodeNew (NULL);
+ dst->choice = ParseDest_featqual;
+ dst->data.ptrvalue = ffp;
+ break;
+ }
+ break;
+ case eParseDstDialog_featqual:
ffp = FeatureFieldLegalNew ();
vnp = (ValNodePtr) DialogToPointer (dlg->feature_type_choice);
if (vnp != NULL) {
@@ -11956,7 +12669,23 @@ static Pointer DialogToParseDst (DialoG d)
dst->choice = ParseDest_featqual;
dst->data.ptrvalue = ffp;
break;
- case 4:
+ case eParseDstDialog_featnote:
+ ffp = FeatureFieldLegalNew ();
+ vnp = (ValNodePtr) DialogToPointer (dlg->feature_note);
+ if (vnp != NULL) {
+ ffp->type = vnp->choice;
+ vnp = ValNodeFree (vnp);
+ }
+ ffp->field = Feat_qual_legal_note;
+ dst = ValNodeNew (NULL);
+ dst->choice = ParseDest_featqual;
+ dst->data.ptrvalue = ffp;
+ break;
+ case eParseDstDialog_commentdesc:
+ dst = ValNodeNew (NULL);
+ dst->choice = ParseDest_comment_descriptor;
+ break;
+ case eParseDstDialog_dbxref:
dst = ValNodeNew (NULL);
dst->choice = ParseDest_dbxref;
dst->data.ptrvalue = SaveStringFromText (dlg->dbxref_db);
@@ -11976,24 +12705,28 @@ static ValNodePtr TestParseDstDialog (DialoG d)
if (dlg == NULL) return NULL;
val = GetValue (dlg->main_choice);
- if (val < 1 || val > 4) {
+ if (val < 1 || val > eParseDstDialog_last) {
ValNodeAddPointer (&err_list, 0, "main choice");
- } else if (val == 2) {
+ } else if (val == eParseDstDialog_srcqual) {
ValNodeLink (&err_list, TestDialog (dlg->src_qual_choice));
- } else if (val == 3) {
+ } else if (val == eParseDstDialog_rnafield) {
+ ValNodeLink (&err_list, TestDialog (dlg->rna_field));
+ } else if (val == eParseDstDialog_featqual) {
ValNodeLink (&err_list, TestDialog (dlg->feature_type_choice));
ValNodeLink (&err_list, TestDialog (dlg->feature_field_choice));
- } else if (val == 4 && TextHasNoText (dlg->dbxref_db)) {
+ } else if (val == eParseDstDialog_featnote) {
+ ValNodeLink (&err_list, TestDialog (dlg->feature_note));
+ } else if (val == eParseDstDialog_dbxref && TextHasNoText (dlg->dbxref_db)) {
ValNodeAddPointer (&err_list, 0, "dbxref db");
}
return err_list;
}
-
+
static DialoG ParseDstDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
{
ParseDstDlgPtr dlg;
- GrouP p, g;
+ GrouP p, g, g2;
ValNodePtr qual_list;
p = HiddenGroup (h, 2, 0, NULL);
@@ -12011,22 +12744,37 @@ static DialoG ParseDstDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Point
dlg->main_choice = PopupList (p, TRUE, ChangeParseDstDialogPopup);
SetObjectExtra (dlg->main_choice, dlg, NULL);
- PopupItem (dlg->main_choice, "Defline");
+ PopupItem (dlg->main_choice, "Definition Line");
+ PopupItem (dlg->main_choice, "Biosource");
PopupItem (dlg->main_choice, "Source Qualifier");
+ PopupItem (dlg->main_choice, "Gene Field");
+ PopupItem (dlg->main_choice, "RNA Field");
+ PopupItem (dlg->main_choice, "CDS Comment");
+ PopupItem (dlg->main_choice, "Protein Field");
PopupItem (dlg->main_choice, "Feature Qualifier");
+ PopupItem (dlg->main_choice, "Feature Note");
+ PopupItem (dlg->main_choice, "Comment Descriptor");
PopupItem (dlg->main_choice, "Dbxref");
SetValue (dlg->main_choice, 1);
g = HiddenGroup (p, 0, 0, NULL);
dlg->src_grp = HiddenGroup (g, -1, 0, NULL);
+ g2 = HiddenGroup (dlg->src_grp, 0, 0, NULL);
qual_list = GetSourceQualList (FALSE);
- dlg->src_qual_choice = ValNodeSelectionDialog (dlg->src_grp, qual_list, SHORT_SELECTION_LIST,
+ dlg->src_qual_choice = ValNodeSelectionDialog (g2, qual_list, SHORT_SELECTION_LIST,
ValNodeStringName,
ValNodeSimpleDataFree,
ValNodeStringCopy,
ValNodeStringMatch,
"source qual",
change_notify, change_userdata, FALSE);
+ dlg->biosrc_list = PopupList (g2, TRUE, ChangeParseDstDialogPopup);
+ SetObjectExtra (dlg->biosrc_list, dlg, NULL);
+ PopupItem (dlg->biosrc_list, "Organism Name");
+ PopupItem (dlg->biosrc_list, "Lineage");
+ PopupItem (dlg->biosrc_list, "Division");
+ SetValue (dlg->biosrc_list, 1);
+
dlg->feat_or_desc = HiddenGroup (dlg->src_grp, 3, 0, NULL);
RadioButton (dlg->feat_or_desc, "Descriptors and Features");
RadioButton (dlg->feat_or_desc, "Descriptors Only");
@@ -12035,11 +12783,43 @@ static DialoG ParseDstDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Point
AlignObjects (ALIGN_CENTER, (HANDLE) dlg->src_qual_choice, (HANDLE) dlg->feat_or_desc, NULL);
Hide (dlg->src_grp);
+ dlg->gene_field = PopupList (g, TRUE, ChangeParseDstDialogPopup);
+ SetObjectExtra (dlg->gene_field, dlg, NULL);
+ PopupItem (dlg->gene_field, "locus");
+ PopupItem (dlg->gene_field, "description");
+ PopupItem (dlg->gene_field, "comment");
+ PopupItem (dlg->gene_field, "allele");
+ PopupItem (dlg->gene_field, "maploc");
+ PopupItem (dlg->gene_field, "locus_tag");
+ PopupItem (dlg->gene_field, "synonym");
+ PopupItem (dlg->gene_field, "old_locus_tag");
+ SetValue (dlg->gene_field, 1);
+ Hide (dlg->gene_field);
+
+ dlg->rna_field = RnaQualDialog (g, "RNA Type", change_notify, change_userdata);
+ Hide (dlg->rna_field);
+
+ dlg->protein_field = PopupList (g, TRUE, ChangeParseDstDialogPopup);
+ SetObjectExtra (dlg->protein_field, dlg, NULL);
+ PopupItem (dlg->protein_field, "name");
+ PopupItem (dlg->protein_field, "description");
+ PopupItem (dlg->protein_field, "E.C. number");
+ PopupItem (dlg->protein_field, "activity");
+ PopupItem (dlg->protein_field, "comment");
+ PopupItem (dlg->protein_field, "mat_peptide name");
+ PopupItem (dlg->protein_field, "mat_peptide description");
+ PopupItem (dlg->protein_field, "mat_peptide comment");
+ SetValue (dlg->protein_field, 1);
+ Hide (dlg->protein_field);
+
dlg->feature_field_grp = HiddenGroup (g, 2, 0, NULL);
dlg->feature_type_choice = FeatureTypeDialog (dlg->feature_field_grp, change_notify, change_userdata);
dlg->feature_field_choice = LegalFeatQualChoiceDialog (dlg->feature_field_grp, change_notify, change_userdata);
Hide (dlg->feature_field_grp);
+ dlg->feature_note = FeatureTypeDialog (g, change_notify, change_userdata);
+ Hide (dlg->feature_note);
+
dlg->dbxref_db = DialogText (g, "", 20, ChangeParseDstDialogText);
SetObjectExtra (dlg->dbxref_db, dlg, NULL);
Hide (dlg->dbxref_db);
@@ -12165,9 +12945,10 @@ static ValNodePtr TestParseActionDialog (DialoG d)
static DialoG
-ParseActionDialog
+ParseActionDialogEx
(GrouP h,
Boolean indexer_version,
+ Boolean use_existing_text,
Nlm_ChangeNotifyProc change_notify,
Pointer change_userdata)
{
@@ -12194,7 +12975,7 @@ ParseActionDialog
dlg->src = ParseSrcDialog (g, change_notify, change_userdata);
StaticPrompt (g, "And place in", 0, popupMenuHeight, programFont, 'r');
dlg->dst = ParseDstDialog (g, change_notify, change_userdata);
- dlg->cap_change = NormalGroup (p, 3, 0, "Capitalization", programFont, NULL);
+ dlg->cap_change = NormalGroup (p, 4, 0, "Capitalization", programFont, NULL);
SetGroupSpacing (dlg->cap_change, 10, 10);
RadioButton (dlg->cap_change, "No change");
@@ -12205,20 +12986,32 @@ ParseActionDialog
dlg->remove_from_parsed = CheckBox (p, "Remove from parsed field", NULL);
- dlg->existing_text = ExistingTextDialog (p, change_notify, change_userdata);
-
+ if (use_existing_text) {
+ dlg->existing_text = ExistingTextDialog (p, change_notify, change_userdata);
+ }
AlignObjects (ALIGN_CENTER, (HANDLE) dlg->cap_change,
(HANDLE) dlg->remove_from_parsed,
- (HANDLE) dlg->existing_text,
(HANDLE) dlg->text_portion,
(HANDLE) g,
+ (HANDLE) dlg->existing_text,
NULL);
return (DialoG) p;
}
-
+
+static DialoG
+ParseActionDialog
+(GrouP h,
+ Boolean indexer_version,
+ Nlm_ChangeNotifyProc change_notify,
+ Pointer change_userdata)
+{
+ return ParseActionDialogEx (h, indexer_version, TRUE, change_notify, change_userdata);
+}
+
+
typedef struct editmacroaction {
PopuP action_type;
@@ -12320,6 +13113,14 @@ static void RunMacroInEditor (ButtoN b)
action->choice = MacroActionChoice_convert_feature;
action->data.ptrvalue = DialogToPointer (e->action_dlg);
break;
+ case 13:
+ action->choice = MacroActionChoice_remove_descriptor;
+ action->data.ptrvalue = DialogToPointer (e->action_dlg);
+ break;
+ case 14:
+ action->choice = MacroActionChoice_autodef;
+ action->data.ptrvalue = DialogToPointer (e->action_dlg);
+ break;
}
sep_list = GetViewedSeqEntryList ();
@@ -12461,6 +13262,8 @@ BuildEditMacroActionWindow
EditFeatureLocationActionPtr edit_loc = NULL;
ConvertFeatureActionPtr convert_feat = NULL;
ParseActionPtr parse = NULL;
+ RemoveDescriptorActionPtr remove_desc = NULL;
+ AutodefActionPtr autodef = NULL;
WindoW w;
GrouP h, c;
ButtoN b;
@@ -12488,6 +13291,8 @@ BuildEditMacroActionWindow
PopupItem (d->action_type, "Remove Feature");
PopupItem (d->action_type, "Edit Feature Location");
PopupItem (d->action_type, "Convert Feature");
+ PopupItem (d->action_type, "Remove Descriptor");
+ PopupItem (d->action_type, "Autodef");
if (d->action_copy == NULL) {
SetValue (d->action_type, 1);
@@ -12546,6 +13351,14 @@ BuildEditMacroActionWindow
SetValue (d->action_type, 12);
convert_feat = (ConvertFeatureActionPtr) d->action_copy->data.ptrvalue;
break;
+ case MacroActionChoice_remove_descriptor:
+ SetValue (d->action_type, 13);
+ remove_desc = (RemoveDescriptorActionPtr) d->action_copy->data.ptrvalue;
+ break;
+ case MacroActionChoice_autodef:
+ SetValue (d->action_type, 14);
+ autodef = (AutodefActionPtr) d->action_copy->data.ptrvalue;
+ break;
default:
SetValue (d->action_type, 1);
break;
@@ -12586,6 +13399,13 @@ BuildEditMacroActionWindow
d->action_dlg = ConvertFeatureActionDialog (h, d->indexer_version, EnableEditMacroActionAccept, d);
PointerToDialog (d->action_dlg, convert_feat);
break;
+ case 13:
+ d->action_dlg = RemoveDescriptorActionDialog (h, d->indexer_version, EnableEditMacroActionAccept, d);
+ PointerToDialog (d->action_dlg, remove_desc);
+ break;
+ case 14:
+ d->action_dlg = AutodefActionDialog (h, d->indexer_version, EnableEditMacroActionAccept, d);
+ break;
}
c = HiddenGroup (h, 4, 0, NULL);
SetGroupSpacing (c, 10, 10);
@@ -12688,6 +13508,14 @@ static Boolean EditMacroAction (ValNodePtr action, Boolean indexer_version)
d.action_copy = ValNodeNew (NULL);
d.action_copy->choice = MacroActionChoice_convert_feature;
d.action_copy->data.ptrvalue = BuildDefaultConvertFeatureAction ();
+ } else if (action_type == 13) {
+ d.action_copy = ValNodeNew (NULL);
+ d.action_copy->choice = MacroActionChoice_remove_descriptor;
+ d.action_copy->data.ptrvalue = BuildDefaultRemoveDescriptorAction ();
+ } else if (action_type == 14) {
+ d.action_copy = ValNodeNew (NULL);
+ d.action_copy->choice = MacroActionChoice_autodef;
+ d.action_copy->data.ptrvalue = BuildDefaultAutodefAction ();
}
}
@@ -12724,6 +13552,12 @@ static Boolean EditMacroAction (ValNodePtr action, Boolean indexer_version)
case MacroActionChoice_convert_feature:
action->data.ptrvalue = ConvertFeatureActionFree (action->data.ptrvalue);
break;
+ case MacroActionChoice_remove_descriptor:
+ action->data.ptrvalue = RemoveDescriptorActionFree(action->data.ptrvalue);
+ break;
+ case MacroActionChoice_autodef:
+ action->data.ptrvalue = AutodefActionFree (action->data.ptrvalue);
+ break;
}
switch (GetValue (d.action_type)) {
case 1:
@@ -12756,6 +13590,14 @@ static Boolean EditMacroAction (ValNodePtr action, Boolean indexer_version)
action->choice = MacroActionChoice_convert_feature;
action->data.ptrvalue = DialogToPointer (d.action_dlg);
break;
+ case 13:
+ action->choice = MacroActionChoice_remove_descriptor;
+ action->data.ptrvalue = DialogToPointer (d.action_dlg);
+ break;
+ case 14:
+ action->choice = MacroActionChoice_autodef;
+ action->data.ptrvalue = DialogToPointer (d.action_dlg);
+ break;
}
}
Remove (w);
@@ -12849,6 +13691,14 @@ static void AddMacroActions (MacroEditorFormPtr f, Int2 item)
d.action_copy = ValNodeNew (NULL);
d.action_copy->choice = MacroActionChoice_convert_feature;
d.action_copy->data.ptrvalue = BuildDefaultConvertFeatureAction();
+ } else if (action_type == 13) {
+ d.action_copy = ValNodeNew (NULL);
+ d.action_copy->choice = MacroActionChoice_remove_descriptor;
+ d.action_copy->data.ptrvalue = BuildDefaultRemoveDescriptorAction();
+ } else if (action_type == 14) {
+ d.action_copy = ValNodeNew (NULL);
+ d.action_copy->choice = MacroActionChoice_autodef;
+ d.action_copy->data.ptrvalue = BuildDefaultAutodefAction();
}
}
@@ -12912,6 +13762,14 @@ static void AddMacroActions (MacroEditorFormPtr f, Int2 item)
new_action->choice = MacroActionChoice_convert_feature;
new_action->data.ptrvalue = DialogToPointer (d.action_dlg);
break;
+ case 13:
+ new_action->choice = MacroActionChoice_remove_descriptor;
+ new_action->data.ptrvalue = DialogToPointer (d.action_dlg);
+ break;
+ case 14:
+ new_action->choice = MacroActionChoice_autodef;
+ new_action->data.ptrvalue = DialogToPointer (d.action_dlg);
+ break;
}
/* add action to macro list */
if (prev_action == NULL) {
@@ -14795,6 +15653,10 @@ SingleMacroAction (Uint2 entityID, Boolean indexer_version)
frm->no_callback = FALSE;
ChangeSingleMacroActionPopup (frm->action_type);
+#ifndef WIN_MAC
+ CreateStdEditorFormMenus (w);
+#endif
+
return (ForM) w;
}
@@ -14817,6 +15679,199 @@ NLM_EXTERN void SingleAECRMacroAction (Uint2 entityID, Boolean indexer_version,
}
+typedef struct singleparseactionfrm {
+ FORM_MESSAGE_BLOCK
+ DialoG dlg;
+ ButtoN leave_dlg_up;
+ ButtoN accept_btn;
+} SingleParseActionFrmData, PNTR SingleParseActionFrmPtr;
+
+
+static void ChangeSingleParseAction (Pointer data)
+{
+ SingleParseActionFrmPtr frm;
+ ValNodePtr err_list;
+
+ frm = (SingleParseActionFrmPtr) data;
+ if (frm == NULL) {
+ return;
+ }
+
+ /* enable or disable accept button */
+ err_list = TestDialog (frm->dlg);
+ if (err_list == NULL) {
+ Enable (frm->accept_btn);
+ } else {
+ Disable (frm->accept_btn);
+ }
+ err_list = ValNodeFree (err_list);
+}
+
+
+static void ClearSingleParseAction (ButtoN b)
+{
+ SingleParseActionFrmPtr frm;
+
+ frm = (SingleParseActionFrmPtr) GetObjectExtra (b);
+ if (frm == NULL) {
+ return;
+ }
+
+ PointerToDialog (frm->dlg, NULL);
+ ChangeSingleParseAction (frm);
+}
+
+
+static void ClearTextSingleParseAction (ButtoN b)
+{
+ SingleParseActionFrmPtr frm;
+ ParseActionPtr parse;
+
+ frm = (SingleParseActionFrmPtr) GetObjectExtra (b);
+ if (frm == NULL) {
+ return;
+ }
+
+ parse = DialogToPointer (frm->dlg);
+
+ if (parse != NULL && parse->portion != NULL) {
+ parse->portion->left_text = MemFree (parse->portion->left_text);
+ parse->portion->right_text = MemFree (parse->portion->right_text);
+ PointerToDialog (frm->dlg, parse);
+ parse = ParseActionFree (parse);
+ ChangeSingleParseAction (frm);
+ }
+}
+
+
+static void ActionToSingleParseActionForm (ForM f, Pointer data)
+{
+ SingleParseActionFrmPtr frm;
+ ParseActionPtr parse;
+
+
+ frm = (SingleParseActionFrmPtr) GetObjectExtra (f);
+ if (frm == NULL) return;
+
+ parse = (ParseActionPtr) data;
+
+ PointerToDialog (frm->dlg, parse);
+ ChangeSingleParseAction (frm);
+}
+
+
+static Pointer FormToParseAction (ForM f)
+{
+ SingleParseActionFrmPtr frm;
+ ParseActionPtr parse;
+
+
+ frm = (SingleParseActionFrmPtr) GetObjectExtra (f);
+ if (frm == NULL) return NULL;
+
+ parse = DialogToPointer (frm->dlg);
+ return parse;
+}
+
+
+
+static void SingleParseAcceptButton (ButtoN b)
+{
+ SingleParseActionFrmPtr frm;
+ ParseActionPtr parse;
+ AECRSamplePtr sample;
+ SeqEntryPtr sep;
+ ValNodePtr vnp;
+ Int4 num_fields = 0, num_feat = 0;
+
+ frm = (SingleParseActionFrmPtr) GetObjectExtra (b);
+ if (frm == NULL) {
+ return;
+ }
+
+ sep = GetTopSeqEntryForEntityID (frm->input_entityID);
+
+ parse = DialogToPointer (frm->dlg);
+ if (parse == NULL) {
+ return;
+ }
+
+ /* check for existing text, then set value in parse*/
+ sample = GetExistingTextForParseAction (parse, sep);
+ if (sample != NULL && sample->num_found > 0) {
+ parse->existing_text = TwoStepExistingText (sample->num_found, FALSE, FALSE);
+ } else {
+ parse->existing_text = ExistingTextOption_replace_old;
+ }
+ sample = AECRSampleFree (sample);
+ if (parse->existing_text == 0) {
+ parse = ParseActionFree (parse);
+ return;
+ }
+
+ vnp = ValNodeNew (NULL);
+ vnp->choice = MacroActionChoice_parse;
+ vnp->data.ptrvalue = parse;
+
+ ApplyMacroToSeqEntry (sep, vnp, &num_fields, &num_feat);
+
+ vnp = MacroActionChoiceFree (vnp);
+
+ ObjMgrSetDirtyFlag (frm->input_entityID, TRUE);
+ ObjMgrSendMsg (OM_MSG_UPDATE, frm->input_entityID, 0, 0);
+ if (!GetStatus (frm->leave_dlg_up)) {
+ Remove (frm->form);
+ }
+ Update ();
+}
+
+
+/* todo - later allow different starting setups */
+NLM_EXTERN ForM SingleParseAction (Uint2 entityID)
+{
+ WindoW w;
+ GrouP h, c, c1;
+ ButtoN b;
+ SingleParseActionFrmPtr frm;
+
+ frm = (SingleParseActionFrmPtr) MemNew (sizeof (SingleParseActionFrmData));
+
+ w = FixedWindow(-20, -13, -10, -10, "Parse Text", StdCloseWindowProc);
+ SetObjectExtra (w, frm, NULL);
+
+ frm->form = (ForM) w;
+ frm->input_entityID = entityID;
+ frm->toform = ActionToSingleParseActionForm;
+ frm->fromform = FormToParseAction;
+
+ h = HiddenGroup (w, -1, 0, NULL);
+ SetGroupSpacing (h, 10, 10);
+
+ frm->dlg = ParseActionDialogEx (h, FALSE, FALSE, ChangeSingleParseAction, frm);
+
+ c1 = HiddenGroup (h, 3, 0, NULL);
+ b = PushButton (c1, "Clear", ClearSingleParseAction);
+ SetObjectExtra (b, frm, NULL);
+ b = PushButton (c1, "Clear Text", ClearTextSingleParseAction);
+ SetObjectExtra (b, frm, NULL);
+ frm->leave_dlg_up = CheckBox (c1, "Leave dialog up", NULL);
+
+
+ c = HiddenGroup (h, 4, 0, NULL);
+ SetGroupSpacing (c, 10, 10);
+ frm->accept_btn = PushButton (c, "Accept", SingleParseAcceptButton);
+ SetObjectExtra (frm->accept_btn, frm, NULL);
+ b = PushButton (c, "Cancel", StdCancelButtonProc);
+
+ AlignObjects (ALIGN_CENTER, (HANDLE) frm->dlg,
+ (HANDLE) c1,
+ (HANDLE) c,
+ NULL);
+
+ return (ForM) w;
+
+}
+
/* Functions for summarizing macro actions for display */
static CharPtr SummarizeExistingText (Uint2 existing_text)
@@ -16058,6 +17113,98 @@ static CharPtr SummarizeRemoveFeatureAction (RemoveFeatureActionPtr a)
}
+static CharPtr SummarizeRemoveDescriptorAction (RemoveDescriptorActionPtr a)
+{
+ CharPtr label = NULL;
+ CharPtr constraint, str;
+ CharPtr fmt = "Remove %s";
+ CharPtr constraint_fmt = "Remove %s descriptors %s";
+
+ if (a == NULL) {
+ str = StringSave ("No action");
+ } else {
+ label = GetDescriptorNameFromDescriptorType (a->type);
+ constraint = SummarizeConstraintSet (a->constraint);
+ if (constraint == NULL) {
+ str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (label)));
+ sprintf (str, fmt, label);
+ } else {
+ str = (CharPtr) MemNew (sizeof (Char) * (StringLen (constraint_fmt) + StringLen (label) + StringLen (constraint)));
+ sprintf (str, constraint_fmt, label, constraint);
+ constraint = MemFree (constraint);
+ }
+ }
+
+ return str;
+}
+
+
+static CharPtr SummarizeAutodefClauseListType (Uint2 clause_list_type)
+{
+ CharPtr str = "complete sequence";
+
+ switch (clause_list_type) {
+ case Autodef_list_type_feature_list:
+ str = "list fFeatures";
+ break;
+ case Autodef_list_type_complete_sequence:
+ str = "complete sequence";
+ break;
+ case Autodef_list_type_complete_genome:
+ str = "complete genome";
+ break;
+ }
+ return str;
+}
+
+
+static CharPtr SummarizeAutodefAction (AutodefActionPtr autodef)
+{
+ CharPtr label = NULL, mod_name;
+ CharPtr str = NULL;
+ CharPtr fmt = "Autodef %s";
+ CharPtr modifiers_fmt = " with modifier";
+ Int4 len;
+ ValNodePtr mod_names = NULL, vnp;
+
+ if (autodef == NULL) {
+ str = StringSave ("No action");
+ } else {
+ label = SummarizeAutodefClauseListType (autodef->clause_list_type);
+ len = StringLen (fmt) + StringLen (label);
+ if (autodef->modifiers != NULL) {
+ len += StringLen (modifiers_fmt) + 2;
+ for (vnp = autodef->modifiers; vnp != NULL; vnp = vnp->next) {
+ mod_name = GetSourceQualName (vnp->data.intvalue);
+ len += StringLen (mod_name) + 3;
+ ValNodeAddPointer (&mod_names, 0, mod_name);
+ }
+ }
+
+ str = (CharPtr) MemNew (sizeof (Char) * (len + 1));
+ sprintf (str, fmt, label);
+
+ if (autodef->modifiers != NULL) {
+ StringCat (str, modifiers_fmt);
+ if (autodef->modifiers->next != NULL) {
+ StringCat (str, "s");
+ }
+ for (vnp = mod_names; vnp != NULL; vnp = vnp->next) {
+ StringCat (str, " ");
+ StringCat (str, vnp->data.ptrvalue);
+ if (vnp->next != NULL) {
+ StringCat (str, ",");
+ }
+ }
+ }
+
+ mod_names = ValNodeFree (mod_names);
+ }
+
+ return str;
+}
+
+
static CharPtr SummarizeConvertSourceOptions (ValNodePtr vnp)
{
ConvertFromCDSOptionsPtr options;
@@ -16421,6 +17568,12 @@ static CharPtr SummarizeMacroAction (ValNodePtr vnp)
case MacroActionChoice_convert_feature:
str = SummarizeConvertFeatureAction (vnp->data.ptrvalue);
break;
+ case MacroActionChoice_remove_descriptor:
+ str = SummarizeRemoveDescriptorAction (vnp->data.ptrvalue);
+ break;
+ case MacroActionChoice_autodef:
+ str = SummarizeAutodefAction (vnp->data.ptrvalue);
+ break;
default:
str = StringSave ("Invalid action");
break;
@@ -16470,7 +17623,8 @@ typedef enum {
eTabColumnConfig_Apply_CDSGeneProtField,
eTabColumnConfig_Apply_FeatureField,
eTabColumnConfig_Apply_PubField,
- eTabColumnConfig_Apply_GenomeProjectId
+ eTabColumnConfig_Apply_GenomeProjectId,
+ eTabColumnConfig_Apply_CommentDescriptor
} ETabColumnConfig;
typedef enum {
@@ -16667,6 +17821,10 @@ static Pointer TabColumnConfigDialogToChoice (DialoG d)
f->field = ValNodeNew (NULL);
f->field->choice = FieldType_misc;
f->field->data.intvalue = Misc_field_genome_project_id;
+ } else if (val == eTabColumnConfig_Apply_CommentDescriptor) {
+ f->field = ValNodeNew (NULL);
+ f->field->choice = FieldType_misc;
+ f->field->data.intvalue = Misc_field_comment_descriptor;
}
if (dlg->erase_when_blank == NULL) {
@@ -16780,6 +17938,7 @@ static void TabColumnActionChange (PopuP p)
Hide (dlg->match_grp);
break;
case eTabColumnConfig_Apply_GenomeProjectId:
+ case eTabColumnConfig_Apply_CommentDescriptor:
Show (dlg->qual_grp);
Hide (dlg->src_qual);
Hide (dlg->feature_field_grp);
@@ -16875,7 +18034,7 @@ static void TabColumnConfigToDialog (DialoG d, Pointer data)
PointerToDialog (dlg->feature_type, NULL);
PointerToDialog (dlg->feature_field, NULL);
} else {
- vn.choice = ff->type;
+ vn.choice = (Uint1) ff->type;
vn.data.ptrvalue = NULL;
vn.next = NULL;
PointerToDialog (dlg->feature_type, &vn);
@@ -16899,6 +18058,8 @@ static void TabColumnConfigToDialog (DialoG d, Pointer data)
PointerToDialog (dlg->pub_field, &vn);
} else if (f->field->choice == FieldType_misc && f->field->data.intvalue == Misc_field_genome_project_id) {
SetValue (dlg->column_action, eTabColumnConfig_Apply_GenomeProjectId);
+ } else if (f->field->choice == FieldType_misc && f->field->data.intvalue == Misc_field_comment_descriptor) {
+ SetValue (dlg->column_action, eTabColumnConfig_Apply_CommentDescriptor);
}
SafeSetStatus (dlg->change_mrna, f->match_mrna);
@@ -17009,6 +18170,7 @@ NLM_EXTERN DialoG TabColumnConfigDialog
PopupItem (dlg->column_action, "Apply to Feature Field");
PopupItem (dlg->column_action, "Apply to Publication Field");
PopupItem (dlg->column_action, "Apply to Genome Project ID");
+ PopupItem (dlg->column_action, "Apply to Comment Descriptor");
SetValue (dlg->column_action, 1);
k = HiddenGroup (p, 0, 0, NULL);
@@ -17405,7 +18567,7 @@ NLM_EXTERN DialoG TabColumnConfigListDialog (GrouP h, ValNodePtr first_values, V
dlg->change_userdata = change_userdata;
- dlg->column_list_doc = DocumentPanel (p, stdCharWidth * 50, stdLineHeight * 12);
+ dlg->column_list_doc = DocumentPanel (p, stdCharWidth * 50, stdLineHeight * 8);
SetObjectExtra (dlg->column_list_doc, dlg, NULL);
SetDocProcs (dlg->column_list_doc, ClickColumnListDoc, NULL, NULL, NULL);
SetDocShade (dlg->column_list_doc, NULL, NULL, ShowSelectedColumn, NULL);
@@ -17449,6 +18611,78 @@ NLM_EXTERN DialoG TabColumnConfigListDialog (GrouP h, ValNodePtr first_values, V
}
+NLM_EXTERN void ChangeDataForTabColumnConfigListDialog (DialoG d, ValNodePtr first_values, ValNodePtr blank_list)
+{
+ TabColumnConfigListDlgPtr dlg;
+ TabColumnConfigPtr PNTR column_list;
+ Int4 num_columns, i;
+ ValNodePtr vnp_v, vnp_b;
+
+ dlg = (TabColumnConfigListDlgPtr) GetObjectExtra (d);
+ if (dlg == NULL) {
+ return;
+ }
+
+ num_columns = ValNodeLen (blank_list);
+ if (num_columns < dlg->num_columns) {
+ /* truncate existing list */
+ for (i = num_columns; i < dlg->num_columns; i++) {
+ dlg->column_list[i] = TabColumnConfigFree (dlg->column_list[i]);
+ dlg->first_values[i] = MemFree (dlg->first_values[i]);
+ }
+ if (dlg->current_column >= num_columns) {
+ dlg->current_column = num_columns - 1;
+ }
+
+ dlg->num_columns = num_columns;
+ } else if (num_columns > dlg->num_columns) {
+ /* need larger lists */
+ for (i = 0; i < dlg->num_columns; i++) {
+ dlg->first_values[i] = MemFree (dlg->first_values[i]);
+ }
+ dlg->first_values = MemFree (dlg->first_values);
+ dlg->first_values = MemNew (sizeof (CharPtr) * num_columns);
+
+ dlg->blank_list = MemFree (dlg->blank_list);
+ dlg->blank_list = (Int4Ptr) MemNew (sizeof (Int4) * num_columns);
+
+ column_list = (TabColumnConfigPtr PNTR) MemNew (sizeof (TabColumnConfigPtr) * num_columns);
+ for (i = 0; i < dlg->num_columns; i++) {
+ column_list[i] = dlg->column_list[i];
+ dlg->column_list[i] = NULL;
+ }
+ dlg->column_list = MemFree (dlg->column_list);
+ dlg->column_list = column_list;
+
+ dlg->num_columns = num_columns;
+ }
+
+ /* populate column list */
+ vnp_v = first_values;
+ vnp_b = blank_list;
+ i = 0;
+ while (vnp_b != NULL) {
+ dlg->blank_list[i] = vnp_b->data.intvalue;
+ if (vnp_v == NULL || StringHasNoText (vnp_v->data.ptrvalue)) {
+ dlg->first_values[i] = StringSave ("First row value is blank");
+ } else {
+ dlg->first_values[i] = StringSave (vnp_v->data.ptrvalue);
+ }
+ vnp_b = vnp_b->next;
+ if (vnp_v != NULL) {
+ vnp_v = vnp_v->next;
+ }
+ i++;
+ }
+
+ PopulateTabConfigListColumnListDoc (d);
+
+ PointerToDialog (dlg->edit_col_dlg, dlg->column_list[dlg->current_column]);
+ SetTabColumnConfigDialogTitle (dlg->edit_col_dlg, dlg->first_values[dlg->current_column], dlg->blank_list[dlg->current_column]);
+
+}
+
+
typedef struct matchtypedlg {
DIALOG_MESSAGE_BLOCK
PopuP match_type;
diff --git a/desktop/macrodlg.h b/desktop/macrodlg.h
index 8818508c..49c1af08 100755
--- a/desktop/macrodlg.h
+++ b/desktop/macrodlg.h
@@ -29,7 +29,7 @@
*
* Version Creation Date: 11/23/2007
*
-* $Revision: 1.11 $
+* $Revision: 1.13 $
*
* File Description:
*
@@ -55,6 +55,7 @@ NLM_EXTERN DialoG TabColumnConfigDialog
Nlm_ChangeNotifyProc change_notify,
Pointer change_userdata);
NLM_EXTERN DialoG TabColumnConfigListDialog (GrouP h, ValNodePtr first_values, ValNodePtr blank_list, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata);
+NLM_EXTERN void ChangeDataForTabColumnConfigListDialog (DialoG d, ValNodePtr first_values, ValNodePtr blank_list);
NLM_EXTERN DialoG MatchTypeDialog (GrouP g, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata);
NLM_EXTERN DialoG FeatureTypeDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata);
@@ -65,4 +66,6 @@ NLM_EXTERN void SingleAECRMacroAction (Uint2 entityID, Boolean indexer_version,
NLM_EXTERN Uint2 TwoStepExistingText (Int4 num_found, Boolean non_text, Boolean allow_multi);
+NLM_EXTERN ForM SingleParseAction (Uint2 entityID);
+
#endif
diff --git a/desktop/salfiles.c b/desktop/salfiles.c
index cd239796..3c9755d8 100644
--- a/desktop/salfiles.c
+++ b/desktop/salfiles.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 1/27/96
*
-* $Revision: 6.101 $
+* $Revision: 6.102 $
*
* File Description:
*
@@ -388,7 +388,7 @@ static SeqEntryPtr NewFastaRead (FILE *fp, Boolean is_na, Boolean parseSeqId, In
if (segcount > segtotal)
segtotal = segcount;
sepnuc = FindNucSeqEntry (lastsep);
- if (IS_Bioseq(sepnuc)) {
+ if (sepnuc != NULL && IS_Bioseq(sepnuc)) {
segbsp=(BioseqPtr)sepnuc->data.ptrvalue;
segsip=segbsp->id;
if (segsip != NULL) {
diff --git a/desktop/salpanel.c b/desktop/salpanel.c
index 472fc76c..58a18e53 100644
--- a/desktop/salpanel.c
+++ b/desktop/salpanel.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 1/27/96
*
-* $Revision: 6.92 $
+* $Revision: 6.93 $
*
* File Description:
*
@@ -6145,7 +6145,8 @@ static void DoApplyFeatureToAlignment (ButtoN b)
if (sfp != NULL
|| (aafdp->feattype == ADD_IMP
- && feature_details_data->featdef_choice == FEATDEF_GENE))
+ && feature_details_data->featdef_choice == FEATDEF_GENE
+ && sep != NULL))
{
if (! StringHasNoText (feature_details_data->geneName) || ! StringHasNoText (feature_details_data->geneDesc))
{
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-26 08:44:48 +0000