From: tcofoegbu Date: Thu, 23 Jul 2015 11:44:08 +0000 (+0100) Subject: Resolved merge conflict in EdtiCommandTest.java X-Git-Tag: Release_2_10_0~563^2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6897b5d861a256c94b23167254c3f4e2ab6acb3a;hp=28fda83cbef0c9c82cd09a343af4e1721085c104;p=jalview.git Resolved merge conflict in EdtiCommandTest.java --- diff --git a/TESTNG b/TESTNG new file mode 100644 index 0000000..f18885f --- /dev/null +++ b/TESTNG @@ -0,0 +1,2 @@ +# Summary of TestNG for this branch +"Functional" Tests: 242 ran, 121 failed. diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java index 2fad332..0022af6 100755 --- a/src/jalview/analysis/AlignmentSorter.java +++ b/src/jalview/analysis/AlignmentSorter.java @@ -820,7 +820,7 @@ public class AlignmentSorter else { // or, also take a look at the scores if necessary. - if (!ignoreScore && sf[f].getScore() != Float.NaN) + if (!ignoreScore && !Float.isNaN(sf[f].getScore())) { if (seqScores[i] == 0) { diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java index 258b8b6..8f24f11 100755 --- a/src/jalview/appletgui/IdPanel.java +++ b/src/jalview/appletgui/IdPanel.java @@ -20,6 +20,13 @@ */ package jalview.appletgui; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.util.UrlLink; +import jalview.viewmodel.AlignmentViewport; + import java.awt.BorderLayout; import java.awt.Panel; import java.awt.event.InputEvent; @@ -29,13 +36,6 @@ import java.awt.event.MouseMotionListener; import java.util.List; import java.util.Vector; -import jalview.datamodel.Sequence; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.util.UrlLink; -import jalview.viewmodel.AlignmentViewport; - public class IdPanel extends Panel implements MouseListener, MouseMotionListener { @@ -142,7 +142,7 @@ public class IdPanel extends Panel implements MouseListener, nl = true; } ; - if (sf[sl].getScore() != Float.NaN && sf[sl].getScore() != 0f) + if (!Float.isNaN(sf[sl].getScore()) && sf[sl].getScore() != 0f) { tooltiptext.append(" Score = "); tooltiptext.append(sf[sl].getScore()); diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java index dae81ef..71ebbb3 100755 --- a/src/jalview/datamodel/Annotation.java +++ b/src/jalview/datamodel/Annotation.java @@ -107,9 +107,13 @@ public class Annotation return; } if (that.displayCharacter != null) + { displayCharacter = new String(that.displayCharacter); + } if (that.description != null) + { description = new String(that.description); + } secondaryStructure = that.secondaryStructure; value = that.value; colour = that.colour; @@ -168,7 +172,7 @@ public class Annotation { sb.append(","); } - if (value != Float.NaN) + if (!Float.isNaN(value)) { sb.append(value); } diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java index 88cb46e..7702792 100755 --- a/src/jalview/io/AnnotationFile.java +++ b/src/jalview/io/AnnotationFile.java @@ -241,7 +241,7 @@ public class AnnotationFile && row.annotations[j].displayCharacter.length() > 0 && !row.annotations[j].displayCharacter .equals(" ")); hasGlyphs |= (row.annotations[j].secondaryStructure != 0 && row.annotations[j].secondaryStructure != ' '); - hasValues |= (row.annotations[j].value != Float.NaN); // NaNs can't + hasValues |= (!Float.isNaN(row.annotations[j].value)); // NaNs can't // be // rendered.. hasText |= (row.annotations[j].description != null && row.annotations[j].description @@ -331,13 +331,13 @@ public class AnnotationFile } if (hasValues) { - if (row.annotations[j].value != Float.NaN) + if (!Float.isNaN(row.annotations[j].value)) { text.append(comma + row.annotations[j].value); } else { - System.err.println("Skipping NaN - not valid value."); + // System.err.println("Skipping NaN - not valid value."); text.append(comma + 0f);// row.annotations[j].value); } comma = ","; diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java index 57f6384..fbe871b 100755 --- a/src/jalview/io/FeaturesFile.java +++ b/src/jalview/io/FeaturesFile.java @@ -1384,7 +1384,7 @@ public class FeaturesFile extends AlignFile out.append(next[j].end); out.append("\t"); out.append(next[j].type); - if (next[j].score != Float.NaN) + if (!Float.isNaN(next[j].score)) { out.append("\t"); out.append(next[j].score); diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java index 7c96d45..6d8ce5f 100644 --- a/src/jalview/io/SequenceAnnotationReport.java +++ b/src/jalview/io/SequenceAnnotationReport.java @@ -152,7 +152,7 @@ public class SequenceAnnotationReport } } // check score should be shown - if (feature.getScore() != Float.NaN) + if (!Float.isNaN(feature.getScore())) { float[][] rng = (minmax == null) ? null : ((float[][]) minmax .get(feature.getType())); diff --git a/src/jalview/io/vamsas/Sequencefeature.java b/src/jalview/io/vamsas/Sequencefeature.java index 3d598d2..ffc9998 100644 --- a/src/jalview/io/vamsas/Sequencefeature.java +++ b/src/jalview/io/vamsas/Sequencefeature.java @@ -20,6 +20,12 @@ */ package jalview.io.vamsas; +import jalview.bin.Cache; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.io.VamsasAppDatastore; +import jalview.util.UrlLink; + import java.util.Enumeration; import java.util.Vector; @@ -31,11 +37,6 @@ import uk.ac.vamsas.objects.core.RangeAnnotation; import uk.ac.vamsas.objects.core.Score; import uk.ac.vamsas.objects.core.Seg; import uk.ac.vamsas.objects.utils.Properties; -import jalview.bin.Cache; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceI; -import jalview.io.VamsasAppDatastore; -import jalview.util.UrlLink; /** * @author JimP @@ -207,7 +208,7 @@ public class Sequencefeature extends Rangetype { for (int i = 0, iSize = feature.links.size(); i < iSize; i++) { - String link = (String) feature.links.elementAt(i); + String link = feature.links.elementAt(i); UrlLink ulink = new UrlLink(link); if (ulink.isValid()) { @@ -220,7 +221,7 @@ public class Sequencefeature extends Rangetype } } dsa.setGroup(feature.getFeatureGroup()); - if (feature.getScore() != Float.NaN) + if (!Float.isNaN(feature.getScore())) { Score fscore = new Score(); dsa.setScore(new Score[] diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java index 7eda2f7..0f2a49c 100644 --- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java +++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java @@ -349,7 +349,7 @@ public class FeatureRenderer extends else if (showFeature(sequenceFeature)) { if (av_isShowSeqFeatureHeight - && sequenceFeature.score != Float.NaN) + && !Float.isNaN(sequenceFeature.score)) { renderScoreFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1, diff --git a/src/jalview/schemes/GraduatedColor.java b/src/jalview/schemes/GraduatedColor.java index 4f1cb58..8a55f79 100644 --- a/src/jalview/schemes/GraduatedColor.java +++ b/src/jalview/schemes/GraduatedColor.java @@ -145,7 +145,7 @@ public class GraduatedColor public boolean isColored(SequenceFeature feature) { float val = feature.getScore(); - if (val == Float.NaN) + if (Float.isNaN(val)) { return true; } @@ -153,7 +153,7 @@ public class GraduatedColor { return true; } - if (this.thrsh == Float.NaN) + if (Float.isNaN(this.thrsh)) { return true; } @@ -211,7 +211,7 @@ public class GraduatedColor return getMaxColor(); } float scr = feature.getScore(); - if (scr == Float.NaN) + if (Float.isNaN(scr)) { return getMinColor(); } diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index 674f3d1..19c6ca8 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -369,7 +369,7 @@ public abstract class FeatureRendererModel implements { allfeatures.add(features[index].getType()); } - if (features[index].score != Float.NaN) + if (!Float.isNaN(features[index].score)) { int nonpos = features[index].getBegin() >= 1 ? 0 : 1; float[][] mm = (float[][]) minmax.get(features[index].getType()); diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java index dfb13a6..91be2e6 100644 --- a/src/jalview/ws/jws2/AADisorderClient.java +++ b/src/jalview/ws/jws2/AADisorderClient.java @@ -265,7 +265,7 @@ public class AADisorderClient extends JabawsCalcWorker implements + rn.from, base + rn.to, methodName); } dseq.addSequenceFeature(sf); - if (last != val && last != Float.NaN) + if (last != val && !Float.isNaN(last)) { fc.put(sf.getType(), sf); } diff --git a/test/jalview/commands/EditCommandTest.java b/test/jalview/commands/EditCommandTest.java index 375ae55..6fa7c22 100644 --- a/test/jalview/commands/EditCommandTest.java +++ b/test/jalview/commands/EditCommandTest.java @@ -31,7 +31,7 @@ public class EditCommandTest private Alignment al; @BeforeMethod(alwaysRun = true) - public void setUp() + public void setUp() { testee = new EditCommand(); seqs = new SequenceI[4];