X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarna.java;h=eb2368daa712ba7f240f9356a82216266ec7a758;hb=c932f0e85a8852824cdd8ce790af68682732c85c;hp=a50de77ae95ed0b247af8b94a86d52623ccc20b3;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java index a50de77..eb2368d 100644 --- a/src/jalview/gui/AppVarna.java +++ b/src/jalview/gui/AppVarna.java @@ -20,23 +20,6 @@ */ package jalview.gui; -import jalview.analysis.AlignSeq; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.ColumnSelection; -import jalview.datamodel.HiddenColumns; -import jalview.datamodel.RnaViewerModel; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.ext.varna.RnaModel; -import jalview.structure.SecondaryStructureListener; -import jalview.structure.SelectionListener; -import jalview.structure.SelectionSource; -import jalview.structure.StructureSelectionManager; -import jalview.structure.VamsasSource; -import jalview.util.Comparison; -import jalview.util.MessageManager; -import jalview.util.ShiftList; - import java.awt.BorderLayout; import java.awt.Color; import java.util.Collection; @@ -60,10 +43,26 @@ import fr.orsay.lri.varna.models.FullBackup; import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.RNA; +import jalview.analysis.AlignSeq; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.RnaViewerModel; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.ext.varna.RnaModel; +import jalview.structure.SecondaryStructureListener; +import jalview.structure.SelectionListener; +import jalview.structure.SelectionSource; +import jalview.structure.StructureSelectionManager; +import jalview.structure.VamsasSource; +import jalview.util.Comparison; +import jalview.util.MessageManager; +import jalview.util.ShiftList; -public class AppVarna extends JInternalFrame implements SelectionListener, - SecondaryStructureListener, InterfaceVARNASelectionListener, - VamsasSource +public class AppVarna extends JInternalFrame + implements SelectionListener, SecondaryStructureListener, + InterfaceVARNASelectionListener, VamsasSource { private static final byte[] PAIRS = new byte[] { '(', ')', '[', ']', '{', '}', '<', '>' }; @@ -120,6 +119,15 @@ public class AppVarna extends JInternalFrame implements SelectionListener, } } + /** + * highlight a region from start to end (inclusive) on rna + * + * @param rna + * @param start + * - first base pair index (from 0) + * @param end + * - last base pair index (from 0) + */ public void highlightRegion(RNA rna, int start, int end) { clearLastSelection(); @@ -177,12 +185,15 @@ public class AppVarna extends JInternalFrame implements SelectionListener, { this(ap); - String sname = aa.sequenceRef == null ? "secondary structure (alignment)" + String sname = aa.sequenceRef == null + ? "secondary structure (alignment)" : seq.getName() + " structure"; String theTitle = sname - + (aa.sequenceRef == null ? " trimmed to " + seq.getName() : ""); + + (aa.sequenceRef == null ? " trimmed to " + seq.getName() + : ""); theTitle = MessageManager.formatMessage("label.varna_params", - new String[] { theTitle }); + new String[] + { theTitle }); setTitle(theTitle); String gappedTitle = sname + " (with gaps)"; @@ -190,7 +201,8 @@ public class AppVarna extends JInternalFrame implements SelectionListener, addModel(gappedModel, gappedTitle); String trimmedTitle = "trimmed " + sname; - RnaModel trimmedModel = new RnaModel(trimmedTitle, aa, seq, null, false); + RnaModel trimmedModel = new RnaModel(trimmedTitle, aa, seq, null, + false); addModel(trimmedModel, trimmedTitle); vab.setSelectedIndex(0); } @@ -203,6 +215,7 @@ public class AppVarna extends JInternalFrame implements SelectionListener, */ protected AppVarna(AlignmentPanel ap) { + this.setFrameIcon(null); this.ap = ap; this.viewId = System.currentTimeMillis() + "." + this.hashCode(); vab = new AppVarnaBinding(); @@ -393,7 +406,8 @@ public class AppVarna extends JInternalFrame implements SelectionListener, RnaModel rnaModel = models.get(rna); if (rnaModel.seq == sequence) { - int highlightPos = rnaModel.gapped ? index : position - 1; + int highlightPos = rnaModel.gapped ? index + : position - sequence.getStart(); mouseOverHighlighter.highlightRegion(rna, highlightPos, highlightPos); vab.updateSelectedRNA(rna); } @@ -414,18 +428,31 @@ public class AppVarna extends JInternalFrame implements SelectionListener, { return; } - if (seqsel != null && seqsel.getSize() > 0) + + RnaModel rnaModel = models.get(rna); + + if (seqsel != null && seqsel.getSize() > 0 + && seqsel.contains(rnaModel.seq)) { int start = seqsel.getStartRes(), end = seqsel.getEndRes(); - ShiftList shift = offsets.get(rna); - if (shift != null) + if (rnaModel.gapped) { - start = shift.shift(start); - end = shift.shift(end); + ShiftList shift = offsets.get(rna); + if (shift != null) + { + start = shift.shift(start); + end = shift.shift(end); + } } + else + { + start = rnaModel.seq.findPosition(start) - rnaModel.seq.getStart(); + end = rnaModel.seq.findPosition(end) - rnaModel.seq.getStart(); + } + selectionHighlighter.highlightRegion(rna, start, end); - selectionHighlighter.getLastHighlight().setOutlineColor( - seqsel.getOutlineColour()); + selectionHighlighter.getLastHighlight() + .setOutlineColor(seqsel.getOutlineColour()); // TODO - translate column markings to positions on structure if present. vab.updateSelectedRNA(rna); } @@ -449,7 +476,7 @@ public class AppVarna extends JInternalFrame implements SelectionListener, if (shift != null) { int i = shift.shift(newBase.getIndex()); - // System.err.println("shifted "+(arg1.getIndex())+" to "+i); + // jalview.bin.Console.errPrintln("shifted "+(arg1.getIndex())+" to "+i); ssm.mouseOverVamsasSequence(seq, i, this); } else @@ -460,7 +487,8 @@ public class AppVarna extends JInternalFrame implements SelectionListener, } @Override - public void onSelectionChanged(BaseList arg0, BaseList arg1, BaseList arg2) + public void onSelectionChanged(BaseList arg0, BaseList arg1, + BaseList arg2) { // TODO translate selected regions in VARNA to a selection on the // alignpanel. @@ -577,7 +605,8 @@ public class AppVarna extends JInternalFrame implements SelectionListener, { if (!model.ann.isValidStruc()) { - throw new IllegalArgumentException("Invalid RNA structure annotation"); + throw new IllegalArgumentException( + "Invalid RNA structure annotation"); } /* @@ -622,11 +651,10 @@ public class AppVarna extends JInternalFrame implements SelectionListener, ShiftList offset = new ShiftList(); int ofstart = -1; int sleng = seq.getLength(); - char[] seqChars = seq.getSequence(); for (int i = 0; i < sleng; i++) { - if (Comparison.isGap(seqChars[i])) + if (Comparison.isGap(seq.getCharAt(i))) { if (ofstart == -1) { @@ -687,7 +715,8 @@ public class AppVarna extends JInternalFrame implements SelectionListener, { if (!model.ann.isValidStruc()) { - throw new IllegalArgumentException("Invalid RNA structure annotation"); + throw new IllegalArgumentException( + "Invalid RNA structure annotation"); } try