X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=aa4be3d73ed924f71e4bca411126e766cbb65296;hb=3b74463d9ba726384240d7707b6ea416a24c6b59;hp=510b21d642e713db46cf60fc6d63ea119b35bfc2;hpb=335e6b12c126bcb6825cd3f66422677db7cd91c7;p=jalview.git diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java index 510b21d..aa4be3d 100644 --- a/test/jalview/project/Jalview2xmlTests.java +++ b/test/jalview/project/Jalview2xmlTests.java @@ -32,7 +32,9 @@ import java.awt.Color; import java.awt.Rectangle; import java.io.File; import java.io.IOException; +import java.math.BigInteger; import java.util.ArrayList; +import java.util.BitSet; import java.util.HashMap; import java.util.List; import java.util.Locale; @@ -59,6 +61,7 @@ import jalview.datamodel.ContactMatrix; import jalview.datamodel.ContactMatrixI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.GeneLocus; +import jalview.datamodel.GroupSet; import jalview.datamodel.HiddenSequences; import jalview.datamodel.Mapping; import jalview.datamodel.PDBEntry; @@ -100,6 +103,7 @@ import jalview.util.MapList; import jalview.util.matcher.Condition; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.seqfeatures.FeatureRendererModel; +import jalview.ws.datamodel.MappableContactMatrixI; import jalview.ws.datamodel.alphafold.PAEContactMatrix; @Test(singleThreaded = true) @@ -110,6 +114,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase @BeforeClass(alwaysRun = true) public void setUpJvOptionPane() { + if (Desktop.instance != null) + Desktop.instance.closeAll_actionPerformed(null); JvOptionPane.setInteractiveMode(false); JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } @@ -243,9 +249,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase 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++) + for (int p = 0, pSize = af.getViewport().getAlignment() + .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++) { if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f)) @@ -264,9 +269,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertTrue(__rcs.isSeqAssociated(), "Group Annotation colourscheme wasn't sequence associated"); - for (int p = 0, - pSize = af.getViewport().getAlignment().getWidth(); p < pSize - && (!diffseqcols || !diffgseqcols); p++) + for (int p = 0, pSize = af.getViewport().getAlignment() + .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++) { if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null, 0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null, @@ -283,12 +287,12 @@ public class Jalview2xmlTests extends Jalview2xmlBase @Test(groups = { "Functional" }) public void gatherViewsHere() throws Exception { - int origCount = Desktop.getAlignFrames() == null ? 0 - : Desktop.getAlignFrames().length; + int origCount = Desktop.getDesktopAlignFrames() == null ? 0 + : Desktop.getDesktopAlignFrames().length; AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( "examples/exampleFile_2_7.jar", DataSourceType.FILE); assertNotNull(af, "Didn't read in the example file correctly."); - assertTrue(Desktop.getAlignFrames().length == 1 + origCount, + assertTrue(Desktop.getDesktopAlignFrames().length == 1 + origCount, "Didn't gather the views in the example file."); } @@ -426,7 +430,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( "examples/exampleFile_2_7.jar", DataSourceType.FILE); - Assert.assertEquals(Desktop.getAlignFrames().length, 1); + Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 1); String afid = af.getViewport().getSequenceSetId(); // check FileLoader returned a reference to the one alignFrame that is @@ -436,8 +440,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase Desktop.explodeViews(af); - int oldviews = Desktop.getAlignFrames().length; - Assert.assertEquals(Desktop.getAlignFrames().length, + int oldviews = Desktop.getDesktopAlignFrames().length; + Assert.assertEquals(Desktop.getDesktopAlignFrames().length, Desktop.getAlignmentPanels(afid).length); File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp"); try @@ -451,14 +455,14 @@ public class Jalview2xmlTests extends Jalview2xmlBase Assert.fail("Didn't save the expanded view state", e); } Desktop.instance.closeAll_actionPerformed(null); - if (Desktop.getAlignFrames() != null) + if (Desktop.getDesktopAlignFrames() != null) { - Assert.assertEquals(Desktop.getAlignFrames().length, 0); + Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0); } af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), DataSourceType.FILE); Assert.assertNotNull(af); - Assert.assertEquals(Desktop.getAlignFrames().length, + Assert.assertEquals(Desktop.getDesktopAlignFrames().length, Desktop.getAlignmentPanels( af.getViewport().getSequenceSetId()).length); Assert.assertEquals(Desktop @@ -515,9 +519,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase Assert.fail("Didn't save the expanded view state", e); } Desktop.instance.closeAll_actionPerformed(null); - if (Desktop.getAlignFrames() != null) + if (Desktop.getDesktopAlignFrames() != null) { - Assert.assertEquals(Desktop.getAlignFrames().length, 0); + Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0); } af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), @@ -694,9 +698,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase Assert.fail("Didn't save the expanded view state", e); } Desktop.instance.closeAll_actionPerformed(null); - if (Desktop.getAlignFrames() != null) + if (Desktop.getDesktopAlignFrames() != null) { - Assert.assertEquals(Desktop.getAlignFrames().length, 0); + Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0); } af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), @@ -788,9 +792,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase Assert.fail("Didn't save the state", e); } Desktop.instance.closeAll_actionPerformed(null); - if (Desktop.getAlignFrames() != null) + if (Desktop.getDesktopAlignFrames() != null) { - Assert.assertEquals(Desktop.getAlignFrames().length, 0); + Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0); } AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded( @@ -1213,7 +1217,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertNotNull(af); AlignmentI ds = null; - for (AlignFrame alignFrame : Desktop.getAlignFrames()) + for (AlignFrame alignFrame : Desktop.getDesktopAlignFrames()) { if (ds == null) { @@ -1559,17 +1563,48 @@ public class Jalview2xmlTests extends Jalview2xmlBase { paevals[i][j] = ((i - j < 2) || ((i > 1 && i < 5) && (j > 1 && i < 5))) ? 1 : 0f; - paevals[j][i] = paevals[i][j]; + paevals[j][i] = -paevals[i][j]; } } PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals); String content = ContactMatrix.contactToFloatString(dummyMat); - Assert.assertTrue(content.contains("\t1.")); // at least one element must be 1 - float[][] vals = ContactMatrix.fromFloatStringToContacts(content, sq.getLength(), sq.getLength()); - assertEquals(vals[3][4],paevals[3][4]); - + Assert.assertTrue(content.contains("\t1.")); // at least one element must be + // 1 + float[][] vals = ContactMatrix.fromFloatStringToContacts(content, + sq.getLength(), sq.getLength()); + assertEquals(vals[3][4], paevals[3][4]); + assertEquals(vals[4][3], paevals[4][3]); + dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, false,0.5f, false)); + Assert.assertNotSame(dummyMat.getNewick(), ""); AlignmentAnnotation paeCm = sq.addContactList(dummyMat); al.addAnnotation(paeCm); + // verify store/restore of group bitsets + for (BitSet gp : dummyMat.getGroups()) + { + StringBuilder sb = new StringBuilder(); + for (long val : gp.toLongArray()) + { + if (sb.length() > 0) + { + sb.append(","); + } + sb.append(val); + } + String[] longvals = sb.toString().split(","); + long[] newlongvals = new long[longvals.length]; + for (int lv = 0; lv < longvals.length; lv++) + { + try + { + newlongvals[lv] = Long.valueOf(longvals[lv]); + } catch (Exception x) + { + Assert.fail("failed to deserialise bitset element "); + } + } + BitSet newGp = BitSet.valueOf(newlongvals); + assertTrue(gp.equals(newGp)); + } File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix", ".jvp"); new Jalview2XML(false).saveState(tfile); @@ -1589,16 +1624,28 @@ public class Jalview2xmlTests extends Jalview2xmlBase ContactMatrixI restoredMat = newSeq .getContactMatrixFor(newSeq.getAnnotation()[0]); Assert.assertNotNull(restoredMat); + MapList oldMap = ((MappableContactMatrixI) dummyMat).getMapFor(sq); + MapList newMap = ((MappableContactMatrixI) restoredMat) + .getMapFor(newSeq); + Assert.assertEquals(oldMap.getFromRanges(), newMap.getFromRanges()); + Assert.assertEquals(oldMap.getToRanges(), newMap.getToRanges()); + Assert.assertEquals(oldMap.getFromRatio(), newMap.getFromRatio()); + Assert.assertEquals(oldMap.getToRatio(), newMap.getToRatio()); for (i = sq.getLength() - 1; i >= 0; i--) { ContactListI oldCM = dummyMat.getContactList(i), newCM = restoredMat.getContactList(i); for (int j = oldCM.getContactHeight(); j >= 0; j--) { - Assert.assertEquals(oldCM.getContactAt(j), newCM.getContactAt(j)); + double old_j = oldCM.getContactAt(j); + double new_j = newCM.getContactAt(j); + Assert.assertEquals(old_j, new_j); } } - + Assert.assertEquals(restoredMat.hasGroups(), dummyMat.hasGroups()); + Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups()); + Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree()); + Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick()); } }