X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=082692400d1840b605d2660f7b9a4c2aa385f6ae;hb=f8c81e5adaada96c5255a539e9d26447bccce3e5;hp=bf2f152dbd64f83626ba4ff8b5707a6fd223e6bf;hpb=358cde16cccc13bcf30494e2b01366bc8e83b43f;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index bf2f152..0826924 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * * This file is part of Jalview. @@ -18,6 +18,7 @@ package jalview.gui; import java.util.*; +import java.util.regex.Pattern; import java.awt.*; import java.awt.datatransfer.*; @@ -104,8 +105,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, { } - BufferedImage bi = new BufferedImage(temp.getHeight(this), temp - .getWidth(this), BufferedImage.TYPE_INT_RGB); + BufferedImage bi = new BufferedImage(temp.getHeight(this), + temp.getWidth(this), BufferedImage.TYPE_INT_RGB); Graphics2D g = (Graphics2D) bi.getGraphics(); g.rotate(Math.toRadians(90)); g.drawImage(temp, 0, -bi.getWidth(this), this); @@ -197,11 +198,6 @@ public class AnnotationLabels extends JPanel implements MouseListener, else if (evt.getActionCommand().equals(HIDE)) { aa[selectedRow].visible = false; - - if (aa[selectedRow].label.equals("Quality")) - { - ap.av.quality = null; - } } else if (evt.getActionCommand().equals(DELETE)) { @@ -245,9 +241,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; } - ap.annotationPanel.adjustPanelHeight(); - ap.annotationScroller.validate(); - ap.paintAlignment(true); + ap.validateAnnotationDimensions(false); + ap.addNotify(); + ap.repaint(); + //validate(); + //ap.paintAlignment(true); } /** @@ -407,22 +405,43 @@ public class AnnotationLabels extends JPanel implements MouseListener, && ap.av.alignment.getAlignmentAnnotation().length > selectedRow) { AlignmentAnnotation aa = ap.av.alignment.getAlignmentAnnotation()[selectedRow]; - - StringBuffer desc = new StringBuffer(""); - + + StringBuffer desc = new StringBuffer(); if (aa.description != null && !aa.description.equals("New description")) { - desc.append(aa.getDescription(true)); - if (aa.hasScore) - desc.append("
"); + // TODO: we could refactor and merge this code with the code in jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature tooltips + desc.append(aa.getDescription(true).trim()); + // check to see if the description is an html fragment. + if (desc.length()<6 || (desc.substring(0,6).toLowerCase().indexOf("")<0)) + { + // clean the description ready for embedding in html + desc = new StringBuffer(Pattern.compile("<").matcher(desc).replaceAll("<")); + desc.insert(0, ""); + } else { + // remove terminating html if any + int i=desc.substring(desc.length()-7).toLowerCase().lastIndexOf(""); + if (i>-1) { + desc.setLength(desc.length()-7+i); + } + } + if (aa.hasScore()) + { + desc.append("
"); + } + + + } else { + // begin the tooltip's html fragment + desc.append(""); } if (aa.hasScore()) { - desc.append("Score: " + aa.score); + // TODO: limit precision of score to avoid noise from imprecise doubles (64.7 becomes 64.7+/some tiny value). + desc.append(" Score: " + aa.score); } - if (desc.length() != 6) + if (desc.length() > 6) { desc.append(""); this.setToolTipText(desc.toString()); @@ -450,11 +469,13 @@ public class AnnotationLabels extends JPanel implements MouseListener, { if (evt.getClickCount() >= 2) { - // todo: make the ap scroll to the selection + // todo: make the ap scroll to the selection - not necessary, first click highlights/scrolls, second selects ap.seqPanel.ap.idPanel.highlightSearchResults(null); ap.av.setSelectionGroup(// new SequenceGroup( - aa[selectedRow].groupRef); // ); + aa[selectedRow].groupRef); // ); ap.paintAlignment(false); + PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); + ap.av.sendSelection(); } else { @@ -478,6 +499,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, SequenceGroup sg = new SequenceGroup(); sg.addSequence(aa[selectedRow].sequenceRef, false); ap.av.setSelectionGroup(sg); + ap.av.sendSelection(); ap.paintAlignment(false); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); } @@ -547,8 +569,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( "Ignore Gaps In Consensus", (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef - .getIgnoreGapsConsensus() - : ap.av.getIgnoreGapsConsensus()); + .getIgnoreGapsConsensus() : ap.av + .getIgnoreGapsConsensus()); final AlignmentAnnotation aaa = aa[selectedRow]; cbmi.addActionListener(new ActionListener() { @@ -571,8 +593,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, if (aaa.groupRef != null) { final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( - "Show Group Histogram", aa[selectedRow].groupRef - .isShowConsensusHistogram()); + "Show Group Histogram", + aa[selectedRow].groupRef.isShowConsensusHistogram()); chist.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -589,10 +611,10 @@ public class AnnotationLabels extends JPanel implements MouseListener, } }); pop.add(chist); - final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( - "Show Group Logo", aa[selectedRow].groupRef - .isShowSequenceLogo()); - cprof.addActionListener(new ActionListener() + final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem( + "Show Group Logo", + aa[selectedRow].groupRef.isShowSequenceLogo()); + cprofl.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { @@ -602,12 +624,12 @@ public class AnnotationLabels extends JPanel implements MouseListener, // view // can be // updated. - aaa.groupRef.setIncludeAllConsSymbols(cprof.getState()); + aaa.groupRef.setshowSequenceLogo(cprofl.getState()); ap.repaint(); // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); } }); - pop.add(cprof); + pop.add(cprofl); } else { @@ -687,8 +709,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, String output = new FormatAdapter().formatSequences("Fasta", seqs, omitHidden); - Toolkit.getDefaultToolkit().getSystemClipboard().setContents( - new StringSelection(output), Desktop.instance); + Toolkit.getDefaultToolkit().getSystemClipboard() + .setContents(new StringSelection(output), Desktop.instance); Vector hiddenColumns = null; if (av.hasHiddenColumns) @@ -821,8 +843,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, g.setColor(aa[gg].annotations[0].colour); } - g.drawLine(x, y - graphExtras - 3, x - + fm.stringWidth(aa[gg].label), y - graphExtras - 3); + g.drawLine(x, y - graphExtras - 3, + x + fm.stringWidth(aa[gg].label), y - graphExtras - 3); g.setColor(Color.black); graphExtras += fontHeight + 8; @@ -843,9 +865,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, else if (dragEvent != null && aa != null) { g.setColor(Color.lightGray); - g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent - .getY() - - scrollOffset); + g.drawString(aa[selectedRow].label, dragEvent.getX(), + dragEvent.getY() - scrollOffset); } if ((aa == null) || (aa.length < 1))