X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=6626016d27fede4ca6bac582a22d1f0de233fb45;hb=aaf78c2f304b237a9c800137126967ace9437c99;hp=bed71d3dbf9b3a23ec55688eae1429e8cc707413;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index bed71d3..6626016 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; @@ -38,6 +37,8 @@ import jalview.io.*; public class AnnotationLabels extends JPanel implements MouseListener, MouseMotionListener, ActionListener { + static String TOGGLE_LABELSCALE = "Scale Label to Column"; + static String ADDNEW = "Add New Row"; static String EDITNAME = "Edit Label/Description"; @@ -72,11 +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) { @@ -101,8 +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); @@ -121,7 +124,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param y - * DOCUMENT ME! + * DOCUMENT ME! */ public void setScrollOffset(int y) { @@ -129,15 +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; @@ -159,7 +170,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void actionPerformed(ActionEvent evt) { @@ -186,11 +197,6 @@ 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)) { @@ -214,30 +220,45 @@ public class AnnotationLabels extends JPanel implements MouseListener, } else if (evt.getActionCommand().equals(COPYCONS_SEQ)) { - SequenceI cons = av.getConsensusSeq(); + SequenceI cons = null; + if (aa[selectedRow].groupRef != null) + { + cons = aa[selectedRow].groupRef.getConsensusSeq(); + } + else + { + cons = av.getConsensusSeq(); + } if (cons != null) { copy_annotseqtoclipboard(cons); } } + else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE)) + { + 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); } /** * 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) { @@ -260,7 +281,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mousePressed(MouseEvent evt) { @@ -272,7 +293,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseReleased(MouseEvent evt) { @@ -285,6 +306,10 @@ 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; @@ -301,7 +326,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseEntered(MouseEvent evt) { @@ -316,7 +341,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseExited(MouseEvent evt) { @@ -331,7 +356,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseDragged(MouseEvent evt) { @@ -367,7 +392,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseMoved(MouseEvent evt) { @@ -409,31 +434,77 @@ 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 > -1 && selectedRow < aa.length) + { + if (aa[selectedRow].groupRef != null) + { + if (evt.getClickCount() >= 2) + { + // 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); // ); + ap.paintAlignment(false); + PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); + ap.av.sendSelection(); + } + else + { + ap.seqPanel.ap.idPanel + .highlightSearchResults(aa[selectedRow].groupRef + .getSequences(null)); + } + return; + } + else if (aa[selectedRow].sequenceRef != null) + { + Vector sr = new Vector(); + sr.addElement(aa[selectedRow].sequenceRef); + if (evt.getClickCount() == 1) + { + 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.av.setSelectionGroup(sg); + ap.av.sendSelection(); + ap.paintAlignment(false); + PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); + } + + } + } + } if (!SwingUtilities.isRightMouseButton(evt)) { return; } - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); - 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); @@ -443,31 +514,145 @@ 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); - // annotation object should be typed - if (selectedRow < aa.length && aa[selectedRow] == ap.av.consensus) + // TODO: annotation object should be typed for autocalculated/derived + // property methods + if (selectedRow < aa.length) { - pop.addSeparator(); - final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( - "Ignore Gaps In Consensus", ap.av.getIgnoreGapsConsensus()); - cbmi.addActionListener(new ActionListener() + if (!aa[selectedRow].autoCalculated) { - public void actionPerformed(ActionEvent e) + if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH) { - ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); + // 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); } - }); - pop.add(cbmi); - final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); - consclipbrd.addActionListener(this); - pop.add(consclipbrd); + } + else if (aa[selectedRow].label.indexOf("Consensus") > -1) + { + pop.addSeparator(); + // av and sequencegroup need to implement same interface for + final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( + "Ignore Gaps In Consensus", + (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef + .getIgnoreGapsConsensus() : ap.av + .getIgnoreGapsConsensus()); + final AlignmentAnnotation aaa = aa[selectedRow]; + cbmi.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + if (aaa.groupRef != null) + { + // TODO: pass on reference to ap so the view can be updated. + aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); + ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + else + { + ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); + } + } + }); + pop.add(cbmi); + // 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 Logo", av.isShowSequenceLogo()); + cprof.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + av.setShowSequenceLogo(cprof.getState()); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(cprof); + } + final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); + consclipbrd.addActionListener(this); + pop.add(consclipbrd); + } } - pop.show(this, evt.getX(), evt.getY()); } @@ -475,7 +660,7 @@ 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) { @@ -502,8 +687,8 @@ 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) @@ -521,7 +706,7 @@ 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 }; } @@ -529,7 +714,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param g1 - * DOCUMENT ME! + * DOCUMENT ME! */ public void paintComponent(Graphics g) { @@ -555,7 +740,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! */ public void drawComponent(Graphics g, int width) { @@ -584,12 +769,14 @@ 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; } @@ -634,8 +821,8 @@ 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; @@ -656,9 +843,8 @@ 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))