+--nonews
+--nosplash
--substitutions
--open={argfiledirname}/sample.a2m
--colour=gecos:flower
---structure={argfiledirname}/test_fab41_unrelaxed_rank_1_model_3.pdb
---paematrix=[label=pAE R1-M3]{argfiledirname}/test_fab41_unrelaxed_rank_1_model_3_scores.json
---structure={argfiledirname}/test_fab41_unrelaxed_rank_2_model_4.pdb
---paematrix=[label=pAE R2-M4]{argfiledirname}/test_fab41_unrelaxed_rank_2_model_4_scores.json
---structure={argfiledirname}/test_fab41_unrelaxed_rank_3_model_2.pdb
---paematrix=[label=pAE R3-M2]{argfiledirname}/test_fab41_unrelaxed_rank_3_model_2_scores.json
---structure={argfiledirname}/test_fab41_unrelaxed_rank_4_model_5.pdb
---paematrix=[label=pAE R4-M5]{argfiledirname}/test_fab41_unrelaxed_rank_4_model_5_scores.json
---structure={argfiledirname}/test_fab41_unrelaxed_rank_5_model_1.pdb
---paematrix=[label=pAE R5-M1]{argfiledirname}/test_fab41_unrelaxed_rank_5_model_1_scores.json
+--structure={dirname}/test_fab41_unrelaxed_rank_1_model_3.pdb
+--paematrix="[label=PAE R1-M3]{dirname}/test_fab41_unrelaxed_rank_1_model_3_scores.json"
+--structure={dirname}/test_fab41_unrelaxed_rank_2_model_4.pdb
+--paematrix="[label=PAE R2-M4]{dirname}/test_fab41_unrelaxed_rank_2_model_4_scores.json"
+--structure={dirname}/test_fab41_unrelaxed_rank_3_model_2.pdb
+--paematrix="[label=PAE R3-M2]{dirname}/test_fab41_unrelaxed_rank_3_model_2_scores.json"
+--structure={dirname}/test_fab41_unrelaxed_rank_4_model_5.pdb
+--paematrix="[label=PAE R4-M5]{dirname}/test_fab41_unrelaxed_rank_4_model_5_scores.json"
+--structure={dirname}/test_fab41_unrelaxed_rank_5_model_1.pdb
+--paematrix="[label=PAE R5-M1]{dirname}/test_fab41_unrelaxed_rank_5_model_1_scores.json"
--image={dirname}/{basename}.html
SequenceI seq = getSpecifiedSequence(af, subId);
if (seq == null)
{
+ // Could not find sequence from subId, let's assume the first
+ // sequence in the alignframe
+ AlignmentI al = af.getCurrentView().getAlignment();
+ seq = al.getSequenceAt(0);
+ }
+
+ if (seq == null)
+ {
Console.warn("Could not find sequence for argument "
+ Arg.STRUCTURE.argString() + "=" + val);
// you probably want to continue here, not break
Console.debug("Using structure file (from argument) '"
+ structureFile.getAbsolutePath() + "'");
}
-
// TRY THIS
/*
* PDBEntry fileEntry = new AssociatePdbFileWithSeq()
* SequenceI[] { selectedSequence });
*
*/
-
/* THIS DOESN'T WORK */
else if (seq.getAllPDBEntries() != null
&& seq.getAllPDBEntries().size() > 0)
}
}
- // load a pAE file if given
+ // load a PAE file if given
if (avm.containsArg(Arg.PAEMATRIX))
{
AlignFrame af = afMap.get(id);
}
String structid = null;
String structfile = null;
- String seqid = null;
+ int seqindex = SubVals.NOTSET;
if (subVals.notSet())
{
ArgValue likelyStructure = avm
else
{
structfile = likelyStructure.getValue();
+ Console.debug(
+ "##### Using closest previous structure argument '"
+ + structfile + "'");
}
}
}
if (structfile != null)
{
Console.info("##### Attaching paeFile '" + paePath + "' to "
- + "structfile=" + subVals.get("structfile"));
+ + "structfile=" + structfile);
EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile, subVals.getIndex(), subVals.get("structfile"),
- true, false, paeLabel);
+ paeFile, seqindex, structfile, true, false, paeLabel);
}
else if (structid != null)
{
Console.info("##### Attaching paeFile '" + paePath + "' to "
- + "structid=" + subVals.get("structid"));
+ + "structid=" + structid);
EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile, subVals.getIndex(), subVals.get("structid"),
- true, true, paeLabel);
+ paeFile, seqindex, subVals.get("structid"), true, true,
+ paeLabel);
}
else
{
+ seqindex = subVals.getIndex();
Console.debug("##### Attaching paeFile '" + paePath
- + "' to sequence index " + subVals.getIndex());
+ + "' to sequence index " + seqindex);
EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile, subVals.getIndex(), null, false, false,
- paeLabel);
- // required to readjust the height and position of the pAE
+ paeFile, seqindex, null, false, false, paeLabel);
+ // required to readjust the height and position of the PAE
// annotation
}
for (AlignmentViewPanel ap : af.getAlignPanels())
private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)
{
+ if (subId == null)
+ return null;
AlignmentI al = af.getCurrentView().getAlignment();
- if (-1 < subId.getIndex()
- && subId.getIndex() < al.getSequences().size())
+ if (subId.has("seqid"))
{
- return al.getSequenceAt(subId.getIndex());
+ return al.findName(subId.get("seqid"));
}
- else if (subId.has("seqid"))
+ else if (-1 < subId.getIndex()
+ && subId.getIndex() < al.getSequences().size())
{
- return al.findName(subId.get("seqid"));
+ return al.getSequenceAt(subId.getIndex());
}
return null;
}
// the counter added to the default linked id prefix
private int defaultLinkedIdCounter = 0;
- // the linked id prefix used for --opennew files
- protected static final String OPENNEWLINKEDIDPREFIX = "OPENNEW:";
+ // the substitution string used to use the defaultLinkedIdCounter
+ private static final String DEFAULTLINKEDIDCOUNTER = "{}";
// the counter added to the default linked id prefix
private int opennewLinkedIdCounter = 0;
+ // the linked id prefix used for --opennew files
+ protected static final String OPENNEWLINKEDIDPREFIX = "OPENNEW:";
+
+ // the counter used for {n} substitutions
+ private int linkedIdAutoCounter = 0;
+
// the linked id substitution string used to increment the idCounter (and use
// the incremented value)
- private static final String INCREMENTAUTOCOUNTERLINKEDID = "{++n}";
+ private static final String INCREMENTLINKEDIDAUTOCOUNTER = "{++n}";
// the linked id substitution string used to use the idCounter
- private static final String AUTOCOUNTERLINKEDID = "{n}";
+ private static final String LINKEDIDAUTOCOUNTER = "{n}";
// the linked id substitution string used to use the base filename of --open
// or --opennew
// --argfile name
private static final String ARGFILEDIRNAME = "{argfiledirname}";
- private int linkedIdAutoCounter = 0;
-
// flag to say whether {n} subtitutions in output filenames should be made.
// Turn on and off with --subs and --nosubs
private boolean substitutions = false;
+ arg);
}
}
- else if (linkedId.contains(AUTOCOUNTERLINKEDID))
+ else if (linkedId.contains(LINKEDIDAUTOCOUNTER))
{
// turn {n} to the autoCounter
autoCounterString = Integer.toString(linkedIdAutoCounter);
- linkedId = linkedId.replace(AUTOCOUNTERLINKEDID,
+ linkedId = linkedId.replace(LINKEDIDAUTOCOUNTER,
autoCounterString);
usingAutoCounterLinkedId = true;
Console.debug(
"Changing linkedId to '" + linkedId + "' from " + arg);
}
- else if (linkedId.contains(INCREMENTAUTOCOUNTERLINKEDID))
+ else if (linkedId.contains(INCREMENTLINKEDIDAUTOCOUNTER))
{
// turn {++n} to the incremented autoCounter
autoCounterString = Integer.toString(++linkedIdAutoCounter);
- linkedId = linkedId.replace(INCREMENTAUTOCOUNTERLINKEDID,
+ linkedId = linkedId.replace(INCREMENTLINKEDIDAUTOCOUNTER,
autoCounterString);
usingAutoCounterLinkedId = true;
Console.debug(
subvals = "";
rest = val;
}
- if (rest.contains(AUTOCOUNTERLINKEDID))
- rest = rest.replace(AUTOCOUNTERLINKEDID,
+ if (rest.contains(LINKEDIDAUTOCOUNTER))
+ rest = rest.replace(LINKEDIDAUTOCOUNTER,
String.valueOf(linkedIdAutoCounter));
- if (rest.contains(INCREMENTAUTOCOUNTERLINKEDID))
- rest = rest.replace(INCREMENTAUTOCOUNTERLINKEDID,
+ if (rest.contains(INCREMENTLINKEDIDAUTOCOUNTER))
+ rest = rest.replace(INCREMENTLINKEDIDAUTOCOUNTER,
String.valueOf(++linkedIdAutoCounter));
- if (rest.contains("{}"))
- rest = rest.replace("{}", String.valueOf(defaultLinkedIdCounter));
+ if (rest.contains(DEFAULTLINKEDIDCOUNTER))
+ rest = rest.replace(DEFAULTLINKEDIDCOUNTER,
+ String.valueOf(defaultLinkedIdCounter));
ArgValuesMap avm = linkedArgs.get(linkedId);
if (avm != null)
{
*/
public class SubVals
{
- private static int NOTSET = -1;
+ public static int NOTSET = -1;
private int index = NOTSET;
import jalview.gui.JvOptionPane;
import jalview.util.ArrayUtils;
-@Test(singleThreaded = true)
+@Test
public class CommandsTest
{
private static final String testfiles = "test/jalview/bin/argparser/testfiles";
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.util;
+
+import java.io.File;
+import java.util.List;
+
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+@Test
+public class FileUtilsTest
+{
+ @Test(groups = "Functional", dataProvider = "patternsAndMinNumFiles")
+ public void testJavaFileGlob(String pattern, int atLeast, int atMost)
+ {
+ List<File> files = FileUtils.getFilesFromGlob(pattern);
+ if (atLeast != -1)
+ {
+ Assert.assertTrue(files.size() > atLeast,
+ "Did not find more than " + atLeast + " files with " + pattern
+ + " (found " + files.size() + ")");
+ }
+ if (atLeast != -1)
+ {
+ Assert.assertTrue(files.size() > atLeast,
+ "Did not find more than " + atLeast + " files with " + pattern
+ + " (found " + files.size() + ")");
+ }
+ if (atMost != -1)
+ {
+ Assert.assertTrue(files.size() < atMost,
+ "Did not find fewer than " + atMost + " files with " + pattern
+ + " (found " + files.size() + ")");
+ }
+ }
+
+ @Test(groups = "Functional", dataProvider = "dirnamesAndBasenames")
+ public void testDirnamesAndBasenames(String filename, int where,
+ String dirname, String basename)
+ {
+ File file = new File(filename);
+ String d = FileUtils.getDirname(file);
+ String b = FileUtils.getBasename(file);
+ Assert.assertEquals(b, basename);
+ if (where == 0)
+ Assert.assertEquals(d, dirname);
+ else if (where < 0)
+ Assert.assertTrue(d.startsWith(dirname),
+ "getDirname(" + file.getPath() + ")=" + d
+ + " didn't start with '" + d + "'");
+ else if (where > 0)
+ Assert.assertTrue(d.endsWith(dirname), "getDirname(" + file.getPath()
+ + ")=" + d + " didn't end with '" + d + "'");
+ }
+
+ @DataProvider(name = "patternsAndMinNumFiles")
+ public Object[][] patternsAndMinNumFiles()
+ {
+ return new Object[][] { { "src/**/*.java", 900, 100000 },
+ { "src/**.java", 900, 100000 },
+ { "test/**/*.java", 250, 2500 },
+ { "test/**.java", 250, 2500 },
+ { "help/**/*.html", 100, 1000 },
+ { "test/**/F*.java", 15, 150 },
+ { "test/jalview/*/F*.java", 10, 15 }, // 12 at time of writing
+ { "test/jalview/**/F*.java", 18, 30 }, // 20 at time of writing
+ { "test/jalview/util/F**.java", 1, 5 }, // 2 at time of writing
+ { "src/jalview/b*/*.java", 14, 19 }, // 15 at time of writing
+ { "src/jalview/b**/*.java", 20, 25 }, // 22 at time of writing
+ };
+ }
+
+ @DataProvider(name = "dirnamesAndBasenames")
+ public Object[][] dirnamesAndBasenames()
+ {
+ return new Object[][] { // -1=startsWith, 0=equals, 1=endsWith
+ { "~/hello/sailor", -1, System.getProperty("user.home"), "sailor" }, //
+ { "~/hello/sailor", 1, "/hello", "sailor" }, //
+ { "./examples/uniref50.fa", -1, "/", "uniref50" }, //
+ { "./examples/uniref50.fa", 1, "/examples", "uniref50" }, //
+ { "examples/uniref50.fa", 1, "/examples", "uniref50" }, //
+ };
+ }
+}
git://source.jalview.org / jalview.git / commitdiff