X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=b77fab6d0e4caae0eb9ebbaa3f1a94a3af8c57e1;hb=e568f853187c30c707c02db4e01a30a7530b74e3;hp=1b5ab8328f84adb4a422ca735cf4b20838958b8d;hpb=f2287ae5b61b6bf36ee90bd6bbf38d44331bf273;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 1b5ab83..b77fab6 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * - * This program 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 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program 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 PURPOSE. See the - * GNU General Public License for more details. + * 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. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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 + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.gui; @@ -74,11 +73,13 @@ public class AnnotationLabels extends JPanel implements MouseListener, Font font = new Font("Arial", Font.PLAIN, 11); + private boolean hasHiddenRows; + /** * Creates a new AnnotationLabels object. * * @param ap - * DOCUMENT ME! + * DOCUMENT ME! */ public AnnotationLabels(AlignmentPanel ap) { @@ -103,8 +104,8 @@ 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); @@ -123,7 +124,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param y - * DOCUMENT ME! + * DOCUMENT ME! */ public void setScrollOffset(int y) { @@ -131,15 +132,23 @@ public class AnnotationLabels extends JPanel implements MouseListener, repaint(); } + /** + * sets selectedRow to -2 if no annotation preset, -1 if no visible row is at + * y + * + * @param y + * coordinate position to search for a row + */ void getSelectedRow(int y) { int height = 0; AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); - + selectedRow = -2; if (aa != null) { for (int i = 0; i < aa.length; i++) { + selectedRow = -1; if (!aa[i].visible) { continue; @@ -161,7 +170,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void actionPerformed(ActionEvent evt) { @@ -217,10 +226,12 @@ public class AnnotationLabels extends JPanel implements MouseListener, else if (evt.getActionCommand().equals(COPYCONS_SEQ)) { SequenceI cons = null; - if (aa[selectedRow].groupRef!=null) + if (aa[selectedRow].groupRef != null) { cons = aa[selectedRow].groupRef.getConsensusSeq(); - } else { + } + else + { cons = av.getConsensusSeq(); } if (cons != null) @@ -231,7 +242,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, } else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE)) { - aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; + aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; } ap.annotationPanel.adjustPanelHeight(); @@ -243,13 +254,14 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ boolean editLabelDescription(AlignmentAnnotation annotation) { EditNameDialog dialog = new EditNameDialog(annotation.label, annotation.description, " Annotation Name ", - "Annotation Description ", "Edit Annotation Name/Description"); + "Annotation Description ", "Edit Annotation Name/Description", + ap.alignFrame); if (!dialog.accept) { @@ -272,7 +284,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mousePressed(MouseEvent evt) { @@ -284,7 +296,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseReleased(MouseEvent evt) { @@ -297,6 +309,10 @@ public class AnnotationLabels extends JPanel implements MouseListener, // Swap these annotations AlignmentAnnotation startAA = ap.av.alignment .getAlignmentAnnotation()[start]; + if (end == -1) + { + end = ap.av.alignment.getAlignmentAnnotation().length - 1; + } AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end]; ap.av.alignment.getAlignmentAnnotation()[end] = startAA; @@ -313,7 +329,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseEntered(MouseEvent evt) { @@ -328,7 +344,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseExited(MouseEvent evt) { @@ -343,7 +359,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseDragged(MouseEvent evt) { @@ -379,7 +395,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseMoved(MouseEvent evt) { @@ -421,43 +437,54 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseClicked(MouseEvent evt) { AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); if (SwingUtilities.isLeftMouseButton(evt)) { - if (selectedRow < aa.length) - { - if (aa[selectedRow].groupRef!=null) + if (selectedRow > -1 && selectedRow < aa.length) + { + if (aa[selectedRow].groupRef != null) { - ap.seqPanel.ap.idPanel.highlightSearchResults(aa[selectedRow].groupRef.getSequences(null)); - if (evt.getClickCount()>=2) + if (evt.getClickCount() >= 2) { // todo: make the ap scroll to the selection - ap.av.setSelectionGroup(new SequenceGroup(aa[selectedRow].groupRef)); + ap.seqPanel.ap.idPanel.highlightSearchResults(null); + ap.av.setSelectionGroup(// new SequenceGroup( + aa[selectedRow].groupRef); // ); + ap.av.sendSelection(); ap.paintAlignment(false); + PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); + } + else + { + ap.seqPanel.ap.idPanel + .highlightSearchResults(aa[selectedRow].groupRef + .getSequences(null)); } return; - } else - if (aa[selectedRow].sequenceRef!=null){ + } + else if (aa[selectedRow].sequenceRef != null) + { Vector sr = new Vector(); sr.addElement(aa[selectedRow].sequenceRef); - if (evt.getClickCount()==1) + if (evt.getClickCount() == 1) { - ap.seqPanel.ap.idPanel.highlightSearchResults(sr); - } else - if (evt.getClickCount()>=2) + ap.seqPanel.ap.idPanel.highlightSearchResults(sr); + } + else if (evt.getClickCount() >= 2) { - ap.seqPanel.ap.idPanel.highlightSearchResults(null); - SequenceGroup sg = new SequenceGroup(); - sg.addSequence(aa[selectedRow].sequenceRef,false); + ap.seqPanel.ap.idPanel.highlightSearchResults(null); + 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()); } - + } } } @@ -466,21 +493,21 @@ public class AnnotationLabels extends JPanel implements MouseListener, return; } - JPopupMenu pop = new JPopupMenu("Annotations"); JMenuItem item = new JMenuItem(ADDNEW); item.addActionListener(this); - - if ((aa == null) || (aa.length == 0)) + pop.add(item); + if (selectedRow < 0) { - item = new JMenuItem(SHOWALL); - item.addActionListener(this); - pop.add(item); + if (hasHiddenRows) + { // let the user make everything visible again + item = new JMenuItem(SHOWALL); + item.addActionListener(this); + pop.add(item); + } pop.show(this, evt.getX(), evt.getY()); return; } - - pop.add(item); item = new JMenuItem(EDITNAME); item.addActionListener(this); pop.add(item); @@ -490,24 +517,31 @@ public class AnnotationLabels extends JPanel implements MouseListener, item = new JMenuItem(DELETE); item.addActionListener(this); pop.add(item); - item = new JMenuItem(SHOWALL); - item.addActionListener(this); - pop.add(item); + if (hasHiddenRows) + { + item = new JMenuItem(SHOWALL); + item.addActionListener(this); + pop.add(item); + } item = new JMenuItem(OUTPUT_TEXT); item.addActionListener(this); pop.add(item); - // TODO: annotation object should be typed for autocalculated/derived property methods + // TODO: annotation object should be typed for autocalculated/derived + // property methods if (selectedRow < aa.length) { - if (!aa[selectedRow].autoCalculated && aa[selectedRow].graph==AlignmentAnnotation.NO_GRAPH) + if (!aa[selectedRow].autoCalculated) { - // display formatting settings for this row. - pop.addSeparator(); - // av and sequencegroup need to implement same interface for - item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE, - aa[selectedRow].scaleColLabel); - item.addActionListener(this); - pop.add(item); + if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH) + { + // display formatting settings for this row. + pop.addSeparator(); + // av and sequencegroup need to implement same interface for + item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE, + aa[selectedRow].scaleColLabel); + item.addActionListener(this); + pop.add(item); + } } else if (aa[selectedRow].label.indexOf("Consensus") > -1) { @@ -516,8 +550,8 @@ 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() { @@ -525,8 +559,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, { if (aaa.groupRef != null) { - // TODO: pass on reference to ap so the view can be updated. - aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); + // TODO: pass on reference to ap so the view can be updated. + aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); } else @@ -539,9 +573,67 @@ public class AnnotationLabels extends JPanel implements MouseListener, // av and sequencegroup need to implement same interface for if (aaa.groupRef != null) { + final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( + "Show Group Histogram", + aa[selectedRow].groupRef.isShowConsensusHistogram()); + chist.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + aaa.groupRef.setShowConsensusHistogram(chist.getState()); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(chist); + final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem( + "Show Group Logo", + aa[selectedRow].groupRef.isShowSequenceLogo()); + cprofl.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + aaa.groupRef.setshowSequenceLogo(cprofl.getState()); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(cprofl); + } + else + { + final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( + "Show Histogram", av.isShowConsensusHistogram()); + chist.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + av.setShowConsensusHistogram(chist.getState()); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(chist); final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( - "Show Full Profile", aa[selectedRow].groupRef - .isIncludeAllConsSymbols()); + "Show Logo", av.isShowSequenceLogo()); cprof.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -552,8 +644,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, // view // can be // updated. - aaa.groupRef.setIncludeAllConsSymbols(cprof.getState()); - ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + av.setShowSequenceLogo(cprof.getState()); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); } }); pop.add(cprof); @@ -570,7 +663,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * do a single sequence copy to jalview and the system clipboard * * @param sq - * sequence to be copied to clipboard + * sequence to be copied to clipboard */ protected void copy_annotseqtoclipboard(SequenceI sq) { @@ -597,8 +690,8 @@ 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) @@ -616,7 +709,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset of a consensus sequence ? need to flag - // sequence as special. + // sequence as special. hiddenColumns }; } @@ -624,7 +717,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param g1 - * DOCUMENT ME! + * DOCUMENT ME! */ public void paintComponent(Graphics g) { @@ -650,7 +743,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! */ public void drawComponent(Graphics g, int width) { @@ -679,12 +772,14 @@ public class AnnotationLabels extends JPanel implements MouseListener, if (aa != null) { + hasHiddenRows = false; for (int i = 0; i < aa.length; i++) { g.setColor(Color.black); if (!aa[i].visible) { + hasHiddenRows = true; continue; } @@ -729,8 +824,8 @@ 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; @@ -751,9 +846,8 @@ 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))