+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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 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;
@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)
{
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;
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
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().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);
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff