From: tcofoegbu Date: Thu, 10 Nov 2016 15:55:51 +0000 (+0000) Subject: Merge branch 'develop' of https://source.jalview.org/git/jalview into develop X-Git-Tag: Release_2_10_1~11^2~7 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3da04c960983caa8614a123b96084933a46a4f46;hp=24667da19e50bd3c663c7b26a1a861568aa0229f;p=jalview.git Merge branch 'develop' of https://source.jalview.org/git/jalview into develop --- diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html index ec1e093..fd6b99f 100755 --- a/help/html/features/featuresFormat.html +++ b/help/html/features/featuresFormat.html @@ -121,11 +121,12 @@ a colour the feature).

- If your sequence annotation is already available in GFF Format (see - gmod.org/wiki/GFF2), then - you can leave it as is, after first adding a line containing only + If your sequence annotation is already available in GFF2 (http://gmod.org/wiki/GFF2) or + GFF3 + (http://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md) format, + then you can leave it as is, after first adding a line containing only 'GFF' after any Jalview feature colour definitions (this - mixed format capability was added in Jalview 2.6). Alternately, + mixed format capability was added in Jalview 2.6). Alternately, you can use Jalview's own sequence feature annotation format, which additionally allows HTML and URLs to be directly attached to each piece of annotation. diff --git a/help/html/features/search.html b/help/html/features/search.html index 9766782..796d623 100755 --- a/help/html/features/search.html +++ b/help/html/features/search.html @@ -73,7 +73,7 @@ td { the match. For example, a simple query like "ACDED" would match all occurences of that string, but "ACD+ED" matches both 'ACDDED' and 'ACDDDDDDDDED'. More usefully, the query - "[ILGVMA]{;5,}" would find stretches of small, hydrophobic + "[GVATC]{;5,}" would find stretches of small, hydrophobic amino acids of at least five residues in length.

The table below describes some of the regular expression syntax:
diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java index f855fde..4d46279 100755 --- a/src/jalview/schemes/ResidueProperties.java +++ b/src/jalview/schemes/ResidueProperties.java @@ -935,7 +935,7 @@ public class ResidueProperties hydrophobic.put("D", ZERO); hydrophobic.put("N", ZERO); hydrophobic.put("S", ZERO); - hydrophobic.put("T", ZERO); + hydrophobic.put("T", ONE); hydrophobic.put("P", ZERO); } diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java index b85536e..c79a043 100644 --- a/test/jalview/bin/CommandLineOperations.java +++ b/test/jalview/bin/CommandLineOperations.java @@ -34,6 +34,15 @@ import org.testng.annotations.Test; public class CommandLineOperations { + private static final int TEST_TIMEOUT = 4500; // Note longer timeout needed on + // full test run than on + // individual tests + + private static final int SETUP_TIMEOUT = 9000; + + private static final int MINFILESIZE_SMALL = 2096; + + private static final int MINFILESIZE_BIG = 4096; private ArrayList successfulCMDs = new ArrayList(); @@ -60,6 +69,7 @@ public class CommandLineOperations this.process = process; } + @Override public void run() { try @@ -142,7 +152,7 @@ public class CommandLineOperations String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props FILE -colour zappo " + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree -dasserver nickname=www.test.com " + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree"; - Worker worker = jalviewDesktopRunner(true, cmds, 9000); + Worker worker = jalviewDesktopRunner(true, cmds, SETUP_TIMEOUT); String ln = null; while ((ln = worker.getOutputReader().readLine()) != null) { @@ -155,7 +165,7 @@ public class CommandLineOperations public void setUpForCommandLineInputOperations() throws IOException { String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats"; - Worker worker = jalviewDesktopRunner(false, cmds, 9000); + Worker worker = jalviewDesktopRunner(false, cmds, SETUP_TIMEOUT); String ln = null; int count = 0; while ((ln = worker.getErrorReader().readLine()) != null) @@ -204,7 +214,8 @@ public class CommandLineOperations worker.process.destroy(); Assert.fail("Jalview did not exit after " + type - + " generation (try running test again to verify - timeout at 9000ms). [" + + " generation (try running test again to verify - timeout at " + + SETUP_TIMEOUT + "ms). [" + harg + "]"); } new File(fileName).delete(); @@ -252,36 +263,36 @@ public class CommandLineOperations { return new Object[][] { { "nodisplay -open examples/uniref50.fa", " -eps", - "test_uniref50_out.eps", true, 4096, 4000 }, + "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT }, { "nodisplay -open examples/uniref50.fa", " -eps", - "test_uniref50_out.eps", false, 4096, 4000 }, + "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT }, { "nogui -open examples/uniref50.fa", " -eps", - "test_uniref50_out.eps", true, 4096, 4000 }, + "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT }, { "nogui -open examples/uniref50.fa", " -eps", - "test_uniref50_out.eps", false, 4096, 4000 }, + "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -eps", - "test_uniref50_out.eps", true, 4096, 4000 }, + "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -svg", - "test_uniref50_out.svg", false, 4096, 3000 }, + "test_uniref50_out.svg", false, MINFILESIZE_BIG, TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -png", - "test_uniref50_out.png", true, 4096, 3000 }, + "test_uniref50_out.png", true, MINFILESIZE_BIG, TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -html", - "test_uniref50_out.html", true, 4096, 3000 }, + "test_uniref50_out.html", true, MINFILESIZE_BIG, TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -fasta", - "test_uniref50_out.mfa", true, 2096, 3000 }, + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL, TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -clustal", - "test_uniref50_out.aln", true, 2096, 3000 }, + "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -msf", - "test_uniref50_out.msf", true, 2096, 3000 }, + "test_uniref50_out.msf", true, MINFILESIZE_SMALL, TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -pileup", - "test_uniref50_out.aln", true, 2096, 3000 }, + "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -pir", - "test_uniref50_out.pir", true, 2096, 3000 }, + "test_uniref50_out.pir", true, MINFILESIZE_SMALL, TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -pfam", - "test_uniref50_out.pfam", true, 2096, 3000 }, + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL, TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -blc", - "test_uniref50_out.blc", true, 2096, 3000 }, + "test_uniref50_out.blc", true, MINFILESIZE_SMALL, TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -jalview", - "test_uniref50_out.jvp", true, 2096, 3000 }, }; + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL, TEST_TIMEOUT }, }; } } diff --git a/test/jalview/schemes/ResiduePropertiesTest.java b/test/jalview/schemes/ResiduePropertiesTest.java index 41d7448..be6a10c 100644 --- a/test/jalview/schemes/ResiduePropertiesTest.java +++ b/test/jalview/schemes/ResiduePropertiesTest.java @@ -1570,7 +1570,7 @@ public class ResiduePropertiesTest checkProperty("polar", "YWHRKTSNDEQ-*X"); checkProperty("positive", "HKR-*"); checkProperty("proline", "P-*"); - checkProperty("hydrophobic", "MILVFYWHKCGAC-*X"); + checkProperty("hydrophobic", "MILVFYWHKTGAC-*X"); } /**