+/*
+ * 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.io;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
import java.io.File;
@BeforeClass
public static void setUpBeforeClass() throws Exception
{
- jalview.bin.Jalview.main(new String[] {"-props","test/src/jalview/io/testProps.jvprops"});
+ jalview.bin.Jalview.main(new String[]
+ { "-props", "test/jalview/io/testProps.jvprops" });
}
/**
@AfterClass
public static void tearDownAfterClass() throws Exception
{
- jalview.gui.Desktop.instance.quit();
+ jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+
}
+
public int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
{
- int numdsann=0;
- for (SequenceI sq: avp.getAlignment().getDataset().getSequences()) {
+ int numdsann = 0;
+ for (SequenceI sq : avp.getAlignment().getDataset().getSequences())
+ {
if (sq.getAnnotation() != null)
{
for (AlignmentAnnotation dssa : sq.getAnnotation())
}
return numdsann;
}
+
@Test
public void testRNAStructureRecovery() throws Exception
{
String inFile = "examples/RF00031_folded.stk";
- String tfile = File.createTempFile("JalviewTest", ".jvp").getAbsolutePath();
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(inFile, FormatAdapter.FILE);
- assertTrue("Didn't read input file "+inFile, af!=null);
- int olddsann=countDsAnn(af.getViewport());
- assertTrue("Didn't find any dataset annotations",olddsann>0);
- assertTrue("Failed to store as a project.",af.saveAlignment(tfile, "Jalview"));
+ String tfile = File.createTempFile("JalviewTest", ".jvp")
+ .getAbsolutePath();
+ AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+ inFile, FormatAdapter.FILE);
+ assertTrue("Didn't read input file " + inFile, af != null);
+ int olddsann = countDsAnn(af.getViewport());
+ assertTrue("Didn't find any dataset annotations", olddsann > 0);
+ af.rnahelicesColour_actionPerformed(null);
+ assertTrue(
+ "Couldn't apply RNA helices colourscheme",
+ af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
+ assertTrue("Failed to store as a project.",
+ af.saveAlignment(tfile, "Jalview"));
+ af.closeMenuItem_actionPerformed(true);
+ af = null;
+ af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
+ FormatAdapter.FILE);
+ assertTrue("Failed to import new project", af != null);
+ int newdsann = countDsAnn(af.getViewport());
+ assertTrue(
+ "Differing numbers of dataset sequence annotation\nOriginally "
+ + olddsann + " and now " + newdsann,
+ olddsann == newdsann);
+ System.out
+ .println("Read in same number of annotations as originally present ("
+ + olddsann + ")");
+ assertTrue(
+ "RNA helices colourscheme was not applied on import.",
+ af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
+ }
+
+ @Test
+ public void testTCoffeeScores() throws Exception
+ {
+ String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
+ String tfile = File.createTempFile("JalviewTest", ".jvp")
+ .getAbsolutePath();
+ AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+ inFile, FormatAdapter.FILE);
+ assertTrue("Didn't read input file " + inFile, af != null);
+ af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
+ assertTrue(
+ "Didn't set T-coffee colourscheme",
+ af.getViewport().getGlobalColourScheme().getClass()
+ .equals(jalview.schemes.TCoffeeColourScheme.class));
+ assertTrue(
+ "Recognise T-Coffee score from string",
+ jalview.schemes.ColourSchemeProperty.getColour(af.getViewport()
+ .getAlignment(),
+ jalview.schemes.ColourSchemeProperty.getColourName(af
+ .getViewport().getGlobalColourScheme())) != null);
+
+ assertTrue("Failed to store as a project.",
+ af.saveAlignment(tfile, "Jalview"));
af.closeMenuItem_actionPerformed(true);
- af=null;
- af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
- assertTrue("Failed to import new project", af!=null);
- int newdsann=countDsAnn(af.getViewport());
- assertTrue("Differing numbers of dataset sequence annotation\nOriginally "+olddsann+" and now "+newdsann,olddsann==newdsann);
- System.out.println("Read in same number of annotations as originally present ("+olddsann+")");
+ af = null;
+ af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
+ FormatAdapter.FILE);
+ assertTrue("Failed to import new project", af != null);
+ assertTrue(
+ "Didn't set T-coffee colourscheme for imported project.",
+ af.getViewport().getGlobalColourScheme().getClass()
+ .equals(jalview.schemes.TCoffeeColourScheme.class));
+ System.out
+ .println("T-Coffee score shading successfully recovered from project.");
}
+ @Test
+ public void testColourByAnnotScores() throws Exception
+ {
+ String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
+ String tfile = File.createTempFile("JalviewTest", ".jvp")
+ .getAbsolutePath();
+ AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+ inFile, FormatAdapter.FILE);
+ assertTrue("Didn't read input file " + inFile, af != null);
+ af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
+ AlignmentAnnotation[] aa = af.getViewport().getAlignment()
+ .getSequenceAt(0).getAnnotation("IUPredWS (Short)");
+ assertTrue(
+ "Didn't find any IUPred annotation to use to shade alignment.",
+ aa != null && aa.length > 0);
+ AnnotationColourGradient cs = new jalview.schemes.AnnotationColourGradient(
+ aa[0], null, AnnotationColourGradient.ABOVE_THRESHOLD);
+ AnnotationColourGradient gcs = new jalview.schemes.AnnotationColourGradient(
+ aa[0], null, AnnotationColourGradient.BELOW_THRESHOLD);
+ cs.setSeqAssociated(true);
+ gcs.setSeqAssociated(true);
+ af.changeColour(cs);
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(57);
+ sg.setEndRes(92);
+ sg.cs = gcs;
+ af.getViewport().getAlignment().addGroup(sg);
+ sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
+ sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
+ af.alignPanel.alignmentChanged();
+ assertTrue("Failed to store as a project.",
+ af.saveAlignment(tfile, "Jalview"));
+ af.closeMenuItem_actionPerformed(true);
+ af = null;
+ af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
+ FormatAdapter.FILE);
+ assertTrue("Failed to import new project", af != null);
+
+ // check for group and alignment colourschemes
+
+ ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
+ ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
+ .get(0).cs;
+ assertTrue("Didn't recover global colourscheme", _rcs != null);
+ assertTrue("Didn't recover annotation colour global scheme",
+ _rcs instanceof AnnotationColourGradient);
+ AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
+ assertTrue("Annotation colourscheme wasn't sequence associated",
+ __rcs.isSeqAssociated());
+
+ boolean diffseqcols = false, diffgseqcols = false;
+ SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
+ for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
+ && (!diffseqcols || !diffgseqcols); p++)
+ {
+ if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0]) != _rcs
+ .findColour(sqs[5].getCharAt(p), p, sqs[5]))
+ {
+ diffseqcols = true;
+ }
+ }
+ assertTrue("Got Different sequence colours", diffseqcols);
+ System.out
+ .println("Per sequence colourscheme (Background) successfully applied and recovered.");
+
+ assertTrue("Didn't recover group colourscheme", _rgcs != null);
+ assertTrue("Didn't recover annotation colour group colourscheme",
+ _rgcs instanceof AnnotationColourGradient);
+ __rcs = (AnnotationColourGradient) _rgcs;
+ assertTrue("Group Annotation colourscheme wasn't sequence associated",
+ __rcs.isSeqAssociated());
+
+ for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
+ && (!diffseqcols || !diffgseqcols); p++)
+ {
+ if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1]) != _rgcs
+ .findColour(sqs[2].getCharAt(p), p, sqs[2]))
+ {
+ diffgseqcols = true;
+ }
+ }
+ assertTrue("Got Different group sequence colours", diffgseqcols);
+ System.out
+ .println("Per sequence (Group) colourscheme successfully applied and recovered.");
+ }
+
+ @Test
+ public void gatherViewsHere() throws Exception
+ {
+ int origCount = Desktop.getAlignframes() == null ? 0 : Desktop
+ .getAlignframes().length;
+ AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+ assertTrue("Didn't read in the example file correctly.", af != null);
+ assertTrue("Didn't gather the views in the example file.",
+ Desktop.getAlignframes().length == 1 + origCount);
+
+ }
+
+ @Test
+ public void viewRefPdbAnnotation() throws Exception
+ {
+ AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+ assertTrue("Didn't read in the example file correctly.", af != null);
+ AlignmentViewPanel sps = null;
+ for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
+ {
+ if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
+ {
+ sps = ap;
+ break;
+ }
+ }
+ assertTrue("Couldn't find the structure view", sps != null);
+ SequenceI sq = sps.getAlignment().findName("1A70|");
+ AlignmentAnnotation refan = null;
+ for (AlignmentAnnotation ra:sps.getAlignment().getAlignmentAnnotation())
+ {
+ if (ra.graph != 0)
+ {
+ refan = ra;
+ break;
+ }
+ }
+ assertTrue("Annotation secondary structure not found.",refan!=null);
+ assertTrue("Couldn't find 1a70 null chain", sq != null);
+ // compare the manually added temperature factor annotation
+ // to the track automatically transferred from the pdb structure on load
+ for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation())
+ {
+ AlignmentAnnotation alaa;
+ sq.addAlignmentAnnotation(alaa = new AlignmentAnnotation(ala));
+ alaa.adjustForAlignment();
+ if (ala.graph == refan.graph)
+ {
+ for (int p = 0; p < ala.annotations.length; p++)
+ {
+ sq.findPosition(p);
+ try {
+ assertTrue(
+ "Mismatch at alignment position " + p,
+ (alaa.annotations[p] == null && refan.annotations[p] == null)
+ || alaa.annotations[p].value == refan.annotations[p].value);
+ }
+ catch (NullPointerException q)
+ {
+ fail("Mismatch of alignment annotations at position " + p
+ + " Ref seq ann: " + refan.annotations[p]
+ + " alignment " + alaa.annotations[p]);
+ }
+ }
+ }
+ }
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff