X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=1577477d78d94a203cfeb18658bd56cb8a78343d;hb=59d682209891099d46b960509907c79e3fb276fe;hp=ff3b0cddd72c6de52c372992de30cd726c084525;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index ff3b0cd..1577477 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -1,13 +1,13 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle * * 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 @@ -23,6 +23,7 @@ import java.util.regex.Pattern; import java.awt.*; import java.awt.datatransfer.*; import java.awt.event.*; +import java.awt.geom.AffineTransform; import java.awt.image.*; import javax.swing.*; @@ -114,6 +115,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, addMouseListener(this); addMouseMotionListener(this); + addMouseWheelListener(ap.annotationPanel); } public AnnotationLabels(AlignViewport av) @@ -143,7 +145,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, void getSelectedRow(int y) { int height = 0; - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); selectedRow = -2; if (aa != null) { @@ -175,20 +178,21 @@ public class AnnotationLabels extends JPanel implements MouseListener, */ public void actionPerformed(ActionEvent evt) { - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); if (evt.getActionCommand().equals(ADDNEW)) { AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null, - null, new Annotation[ap.av.alignment.getWidth()]); + null, new Annotation[ap.av.getAlignment().getWidth()]); if (!editLabelDescription(newAnnotation)) { return; } - ap.av.alignment.addAnnotation(newAnnotation); - ap.av.alignment.setAnnotationIndex(newAnnotation, 0); + ap.av.getAlignment().addAnnotation(newAnnotation); + ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0); } else if (evt.getActionCommand().equals(EDITNAME)) { @@ -201,7 +205,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, } else if (evt.getActionCommand().equals(DELETE)) { - ap.av.alignment.deleteAnnotation(aa[selectedRow]); + ap.av.getAlignment().deleteAnnotation(aa[selectedRow]); } else if (evt.getActionCommand().equals(SHOWALL)) { @@ -244,8 +248,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, ap.validateAnnotationDimensions(false); ap.addNotify(); ap.repaint(); - //validate(); - //ap.paintAlignment(true); + // validate(); + // ap.paintAlignment(true); } /** @@ -305,16 +309,17 @@ public class AnnotationLabels extends JPanel implements MouseListener, if (start != end) { // Swap these annotations - AlignmentAnnotation startAA = ap.av.alignment + AlignmentAnnotation startAA = ap.av.getAlignment() .getAlignmentAnnotation()[start]; if (end == -1) { - end = ap.av.alignment.getAlignmentAnnotation().length - 1; + end = ap.av.getAlignment().getAlignmentAnnotation().length - 1; } - AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end]; + AlignmentAnnotation endAA = ap.av.getAlignment() + .getAlignmentAnnotation()[end]; - ap.av.alignment.getAlignmentAnnotation()[end] = startAA; - ap.av.alignment.getAlignmentAnnotation()[start] = endAA; + ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA; + ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA; } resizePanel = false; @@ -402,42 +407,53 @@ public class AnnotationLabels extends JPanel implements MouseListener, getSelectedRow(evt.getY() - scrollOffset); if (selectedRow > -1 - && ap.av.alignment.getAlignmentAnnotation().length > selectedRow) + && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow) { - AlignmentAnnotation aa = ap.av.alignment.getAlignmentAnnotation()[selectedRow]; - + AlignmentAnnotation aa = ap.av.getAlignment() + .getAlignmentAnnotation()[selectedRow]; + StringBuffer desc = new StringBuffer(); if (aa.description != null && !aa.description.equals("New description")) { - // TODO: we could refactor and merge this code with the code in jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature tooltips + // 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)) + 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 = 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); - } + } + 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 { + + } + else + { // begin the tooltip's html fragment desc.append(""); } if (aa.hasScore()) { - // TODO: limit precision of score to avoid noise from imprecise doubles (64.7 becomes 64.7+/some tiny value). + // TODO: limit precision of score to avoid noise from imprecise doubles + // (64.7 becomes 64.7+/some tiny value). desc.append(" Score: " + aa.score); } @@ -460,7 +476,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, */ public void mouseClicked(MouseEvent evt) { - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); if (SwingUtilities.isLeftMouseButton(evt)) { if (selectedRow > -1 && selectedRow < aa.length) @@ -469,7 +486,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, { if (evt.getClickCount() >= 2) { - // todo: make the ap scroll to the selection - not necessary, first click highlights/scrolls, second selects + // 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); // ); @@ -630,6 +648,28 @@ public class AnnotationLabels extends JPanel implements MouseListener, } }); pop.add(cprofl); + final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem( + "Normalise Group Logo", + aa[selectedRow].groupRef.isNormaliseSequenceLogo()); + cproflnorm.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState()); + // automatically enable logo display if we're clicked + aaa.groupRef.setshowSequenceLogo(true); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(cproflnorm); } else { @@ -646,6 +686,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, // can be // updated. av.setShowConsensusHistogram(chist.getState()); + ap.alignFrame.setMenusForViewport(); ap.repaint(); // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); } @@ -664,11 +705,32 @@ public class AnnotationLabels extends JPanel implements MouseListener, // can be // updated. av.setShowSequenceLogo(cprof.getState()); + ap.alignFrame.setMenusForViewport(); ap.repaint(); // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); } }); pop.add(cprof); + final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem( + "Normalise Logo", av.isNormaliseSequenceLogo()); + cprofnorm.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + av.setShowSequenceLogo(true); + av.setNormaliseSequenceLogo(cprofnorm.getState()); + ap.alignFrame.setMenusForViewport(); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(cprofnorm); } final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); consclipbrd.addActionListener(this); @@ -700,7 +762,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, sq.setDatasetSequence(dseqs[0]); } Alignment ds = new Alignment(dseqs); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, sq.getLength(), seqs); @@ -713,7 +775,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, .setContents(new StringSelection(output), Desktop.instance); Vector hiddenColumns = null; - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { hiddenColumns = new Vector(); for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++) @@ -782,18 +844,22 @@ public class AnnotationLabels extends JPanel implements MouseListener, g.translate(0, scrollOffset); g.setColor(Color.black); - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); int fontHeight = g.getFont().getSize(); int y = 0; int x = 0; int graphExtras = 0; int offset = 0; - + Font baseFont = g.getFont(); + FontMetrics baseMetrics = fm; + int ofontH = fontHeight; + boolean visible = true; if (aa != null) { hasHiddenRows = false; for (int i = 0; i < aa.length; i++) { + visible = true; g.setColor(Color.black); if (!aa[i].visible) @@ -826,30 +892,55 @@ public class AnnotationLabels extends JPanel implements MouseListener, groupSize++; } } - if (groupSize * (fontHeight + 8) < aa[i].height) { graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2; } - - for (int gg = 0; gg < aa.length; gg++) + else { - if (aa[gg].graphGroup == aa[i].graphGroup) + // scale font to fit + float h = aa[i].height / (float) groupSize, s; + if (h < 9) { - x = width - fm.stringWidth(aa[gg].label) - 3; - g.drawString(aa[gg].label, x, y - graphExtras); - if (aa[gg].annotations[0] != null) + visible = false; + } + else + { + fontHeight = -8 + (int) h; + s = ((float) fontHeight) / (float) ofontH; + Font f = baseFont.deriveFont(AffineTransform + .getScaleInstance(s, s)); + g.setFont(f); + fm = g.getFontMetrics(); + graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2; + } + } + if (visible) + { + for (int gg = 0; gg < aa.length; gg++) + { + if (aa[gg].graphGroup == aa[i].graphGroup) { - g.setColor(aa[gg].annotations[0].colour); - } + x = width - fm.stringWidth(aa[gg].label) - 3; + g.drawString(aa[gg].label, x, y - graphExtras); + + if (aa[gg]._linecolour != null) + { - g.drawLine(x, y - graphExtras - 3, - x + fm.stringWidth(aa[gg].label), y - graphExtras - 3); + g.setColor(aa[gg]._linecolour); + g.drawLine(x, y - graphExtras + 3, + x + fm.stringWidth(aa[gg].label), y - graphExtras + + 3); + } - g.setColor(Color.black); - graphExtras += fontHeight + 8; + g.setColor(Color.black); + graphExtras += fontHeight + 8; + } } } + g.setFont(baseFont); + fm = baseMetrics; + fontHeight = ofontH; } else {