X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=8050490426d757e961c2222249b0a55c2491470a;hb=6a7ed84443875e35d61de7f57c4aa6898c68775a;hp=81a3cd2a506b08f3d985f0c7fb8738917fac0660;hpb=890bd0eac47a4b0f55bd062a359c16a43c3780a0;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 81a3cd2..8050490 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -1,17 +1,17 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) + * Copyright (C) 2008 AM Waterhouse, J Procter, 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 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. - * + * * 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 @@ -31,36 +31,52 @@ import jalview.io.*; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ -public class AnnotationLabels - extends JPanel implements MouseListener, - MouseMotionListener, ActionListener +public class AnnotationLabels extends JPanel implements MouseListener, + MouseMotionListener, ActionListener { static String ADDNEW = "Add New Row"; + static String EDITNAME = "Edit Label/Description"; + static String HIDE = "Hide This Row"; + static String DELETE = "Delete This Row"; + static String SHOWALL = "Show All Hidden Rows"; + static String OUTPUT_TEXT = "Export Annotation"; + static String COPYCONS_SEQ = "Copy Consensus Sequence"; + boolean resizePanel = false; + Image image; + AlignmentPanel ap; + AlignViewport av; + boolean resizing = false; + MouseEvent dragEvent; + int oldY; + int selectedRow; + int scrollOffset = 0; + Font font = new Font("Arial", Font.PLAIN, 11); /** * Creates a new AnnotationLabels object. - * - * @param ap DOCUMENT ME! + * + * @param ap + * DOCUMENT ME! */ public AnnotationLabels(AlignmentPanel ap) { @@ -81,14 +97,12 @@ public class AnnotationLabels MediaTracker mt = new MediaTracker(this); mt.addImage(temp, 0); mt.waitForID(0); - } - catch (Exception ex) + } catch (Exception ex) { } - 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); @@ -105,8 +119,9 @@ public class AnnotationLabels /** * DOCUMENT ME! - * - * @param y DOCUMENT ME! + * + * @param y + * DOCUMENT ME! */ public void setScrollOffset(int y) { @@ -142,19 +157,18 @@ public class AnnotationLabels /** * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! */ public void actionPerformed(ActionEvent evt) { - int dif = 0; AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); if (evt.getActionCommand().equals(ADDNEW)) { AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null, - null, - new Annotation[ap.av.alignment.getWidth()]); + null, new Annotation[ap.av.alignment.getWidth()]); if (!editLabelDescription(newAnnotation)) { @@ -163,10 +177,6 @@ public class AnnotationLabels ap.av.alignment.addAnnotation(newAnnotation); ap.av.alignment.setAnnotationIndex(newAnnotation, 0); - if (aa != null) - { - dif = aa[aa.length - 1].height; - } } else if (evt.getActionCommand().equals(EDITNAME)) { @@ -181,33 +191,26 @@ public class AnnotationLabels { ap.av.quality = null; } - - dif = aa[selectedRow].height * -1; } else if (evt.getActionCommand().equals(DELETE)) { ap.av.alignment.deleteAnnotation(aa[selectedRow]); - dif = aa[selectedRow].height * -1; } else if (evt.getActionCommand().equals(SHOWALL)) { for (int i = 0; i < aa.length; i++) { - if (!aa[i].visible) + if (!aa[i].visible && aa[i].annotations != null) { - dif += aa[i].height; aa[i].visible = true; } } } else if (evt.getActionCommand().equals(OUTPUT_TEXT)) { - new AnnotationExporter().exportAnnotations( - ap, - new AlignmentAnnotation[] - {aa[selectedRow]}, - null - ); + new AnnotationExporter().exportAnnotations(ap, + new AlignmentAnnotation[] + { aa[selectedRow] }, null, null); } else if (evt.getActionCommand().equals(COPYCONS_SEQ)) { @@ -226,16 +229,15 @@ public class AnnotationLabels /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ boolean editLabelDescription(AlignmentAnnotation annotation) { EditNameDialog dialog = new EditNameDialog(annotation.label, - annotation.description, - " Annotation Name ", - "Annotation Description ", - "Edit Annotation Name/Description"); + annotation.description, " Annotation Name ", + "Annotation Description ", "Edit Annotation Name/Description"); if (!dialog.accept) { @@ -245,7 +247,7 @@ public class AnnotationLabels annotation.label = dialog.getName(); String text = dialog.getDescription(); - if (text.length() == 0) + if (text != null && text.length() == 0) { text = null; } @@ -256,8 +258,9 @@ public class AnnotationLabels /** * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! */ public void mousePressed(MouseEvent evt) { @@ -267,8 +270,9 @@ public class AnnotationLabels /** * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! */ public void mouseReleased(MouseEvent evt) { @@ -278,9 +282,9 @@ public class AnnotationLabels if (start != end) { - //Swap these annotations - AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[ - start]; + // Swap these annotations + AlignmentAnnotation startAA = ap.av.alignment + .getAlignmentAnnotation()[start]; AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end]; ap.av.alignment.getAlignmentAnnotation()[end] = startAA; @@ -295,8 +299,9 @@ public class AnnotationLabels /** * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! */ public void mouseEntered(MouseEvent evt) { @@ -309,8 +314,9 @@ public class AnnotationLabels /** * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! */ public void mouseExited(MouseEvent evt) { @@ -323,8 +329,9 @@ public class AnnotationLabels /** * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! */ public void mouseDragged(MouseEvent evt) { @@ -338,13 +345,13 @@ public class AnnotationLabels dif /= ap.av.charHeight; dif *= ap.av.charHeight; - if ( (d.height - dif) > 20) + if ((d.height - dif) > 20) { ap.annotationScroller.setPreferredSize(new Dimension(d.width, - d.height - dif)); + d.height - dif)); d = ap.annotationSpaceFillerHolder.getPreferredSize(); ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension( - d.width, d.height - dif)); + d.width, d.height - dif)); ap.paintAlignment(true); } @@ -358,8 +365,9 @@ public class AnnotationLabels /** * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! */ public void mouseMoved(MouseEvent evt) { @@ -368,25 +376,40 @@ public class AnnotationLabels getSelectedRow(evt.getY() - scrollOffset); if (selectedRow > -1 - && ap.av.alignment.getAlignmentAnnotation().length > selectedRow) + && ap.av.alignment.getAlignmentAnnotation().length > selectedRow) { - String desc = ap.av.alignment. - getAlignmentAnnotation()[selectedRow].description; + AlignmentAnnotation aa = ap.av.alignment.getAlignmentAnnotation()[selectedRow]; + + StringBuffer desc = new StringBuffer(""); - if (desc != null && !desc.equals("New description")) + if (aa.description != null + && !aa.description.equals("New description")) { - setToolTipText(ap.av.alignment. - getAlignmentAnnotation()[selectedRow].description); + desc.append(aa.getDescription(true)); + if (aa.hasScore) + desc.append("
"); + } + if (aa.hasScore()) + { + desc.append("Score: " + aa.score); } + if (desc.length() != 6) + { + desc.append(""); + this.setToolTipText(desc.toString()); + } + else + this.setToolTipText(null); } - repaint(); + } /** * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! */ public void mouseClicked(MouseEvent evt) { @@ -397,20 +420,19 @@ public class AnnotationLabels AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); - if ( (aa == null) || (aa.length == 0)) + JPopupMenu pop = new JPopupMenu("Annotations"); + JMenuItem item = new JMenuItem(ADDNEW); + item.addActionListener(this); + + if ((aa == null) || (aa.length == 0)) { - JPopupMenu pop = new JPopupMenu("Annotations"); - JMenuItem item = new JMenuItem(ADDNEW); + item = new JMenuItem(SHOWALL); item.addActionListener(this); pop.add(item); pop.show(this, evt.getX(), evt.getY()); - return; } - JPopupMenu pop = new JPopupMenu("Annotations"); - JMenuItem item = new JMenuItem(ADDNEW); - item.addActionListener(this); pop.add(item); item = new JMenuItem(EDITNAME); item.addActionListener(this); @@ -428,12 +450,11 @@ public class AnnotationLabels item.addActionListener(this); pop.add(item); // annotation object should be typed - if (aa[selectedRow] == ap.av.consensus) + if (selectedRow < aa.length && aa[selectedRow] == ap.av.consensus) { pop.addSeparator(); final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( - "Ignore Gaps In Consensus", - ap.av.getIgnoreGapsConsensus()); + "Ignore Gaps In Consensus", ap.av.getIgnoreGapsConsensus()); cbmi.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -452,25 +473,22 @@ public class AnnotationLabels /** * do a single sequence copy to jalview and the system clipboard - * - * @param sq sequence to be copied to clipboard + * + * @param sq + * sequence to be copied to clipboard */ protected void copy_annotseqtoclipboard(SequenceI sq) { SequenceI[] seqs = new SequenceI[] - { - sq}; + { sq }; String[] omitHidden = null; SequenceI[] dseqs = new SequenceI[] - { - sq.getDatasetSequence()}; + { sq.getDatasetSequence() }; if (dseqs[0] == null) { dseqs[0] = new Sequence(sq); - dseqs[0].setSequence( - jalview.analysis.AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, - sq.getSequenceAsString())); + dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps( + jalview.util.Comparison.GapChars, sq.getSequenceAsString())); sq.setDatasetSequence(dseqs[0]); } @@ -478,16 +496,14 @@ public class AnnotationLabels if (av.hasHiddenColumns) { omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, - sq.getLength(), seqs); + sq.getLength(), seqs); } - String output = new FormatAdapter().formatSequences( - "Fasta", - seqs, - omitHidden); + 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) @@ -495,26 +511,25 @@ public class AnnotationLabels hiddenColumns = new Vector(); for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++) { - int[] region = (int[]) - av.getColumnSelection().getHiddenColumns().elementAt(i); + int[] region = (int[]) av.getColumnSelection().getHiddenColumns() + .elementAt(i); hiddenColumns.addElement(new int[] - {region[0], - region[1]}); + { region[0], region[1] }); } } Desktop.jalviewClipboard = new Object[] - { - seqs, - ds, // what is the dataset of a consensus sequence ? need to flag sequence as special. - hiddenColumns}; + { seqs, ds, // what is the dataset of a consensus sequence ? need to flag + // sequence as special. + hiddenColumns }; } /** * DOCUMENT ME! - * - * @param g1 DOCUMENT ME! + * + * @param g1 + * DOCUMENT ME! */ public void paintComponent(Graphics g) { @@ -529,7 +544,7 @@ public class AnnotationLabels if (av.antiAlias) { g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); + RenderingHints.VALUE_ANTIALIAS_ON); } drawComponent(g2, width); @@ -538,8 +553,9 @@ public class AnnotationLabels /** * DOCUMENT ME! - * - * @param g DOCUMENT ME! + * + * @param g + * DOCUMENT ME! */ public void drawComponent(Graphics g, int width) { @@ -561,32 +577,35 @@ public class AnnotationLabels AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); int fontHeight = g.getFont().getSize(); - int y = fontHeight; + int y = 0; int x = 0; int graphExtras = 0; + int offset = 0; if (aa != null) { for (int i = 0; i < aa.length; i++) { + g.setColor(Color.black); + if (!aa[i].visible) { continue; } - x = width - fm.stringWidth(aa[i].label) - 3; + y += aa[i].height; - if (aa[i].graph > 0 && aa[i].graphHeight > 0) - { - graphExtras = y; - - y += (aa[i].height / 3); + offset = -aa[i].height / 2; - if (aa[i].graphGroup < 0) - { - graphExtras = y + fontHeight; - } + if (aa[i].hasText) + { + offset += fm.getHeight() / 2; + offset -= fm.getDescent(); } + else + offset += fm.getDescent(); + + x = width - fm.stringWidth(aa[i].label) - 3; if (aa[i].graphGroup > -1) { @@ -601,7 +620,7 @@ public class AnnotationLabels if (groupSize * (fontHeight + 8) < aa[i].height) { - graphExtras += (aa[i].height - (groupSize * (fontHeight + 8))) / 2; + graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2; } for (int gg = 0; gg < aa.length; gg++) @@ -609,15 +628,14 @@ public class AnnotationLabels if (aa[gg].graphGroup == aa[i].graphGroup) { x = width - fm.stringWidth(aa[gg].label) - 3; - g.drawString(aa[gg].label, x, graphExtras); + g.drawString(aa[gg].label, x, y - graphExtras); if (aa[gg].annotations[0] != null) { g.setColor(aa[gg].annotations[0].colour); } - g.drawLine(x, graphExtras + 3, - x + fm.stringWidth(aa[gg].label), - graphExtras + 3); + g.drawLine(x, y - graphExtras - 3, x + + fm.stringWidth(aa[gg].label), y - graphExtras - 3); g.setColor(Color.black); graphExtras += fontHeight + 8; @@ -626,38 +644,7 @@ public class AnnotationLabels } else { - g.drawString(aa[i].label, x, y); - } - - if (aa[i].graph > 0) - { - /* if (aa[i].graphLines != null) - { - for (int gl = 0; gl < aa[i].graphLines.size(); gl++) - { - x = width - fm.stringWidth(aa[i].getGraphLine(gl).label) - 3; - g.drawString(aa[i].getGraphLine(gl).label, x, graphExtras); - g.setColor(aa[i].getGraphLine(gl).colour); - Graphics2D g2 = (Graphics2D) g; - g2.setStroke(new BasicStroke(1, - BasicStroke.CAP_SQUARE, - BasicStroke.JOIN_ROUND, 3f, - new float[] - {5f, 3f}, 0f)); - - graphExtras += 3; - - g.drawLine(x, graphExtras, - x+fm.stringWidth(aa[i].label), - graphExtras); - g2.setStroke(new BasicStroke()); - } - }*/ - y += ( (2 * aa[i].height) / 3); - } - else - { - y += aa[i].height; + g.drawString(aa[i].label, x, y + offset); } } } @@ -669,11 +656,12 @@ public class AnnotationLabels 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)) + if ((aa == null) || (aa.length < 1)) { g.drawString("Right click", 2, 8); g.drawString("to add annotation", 2, 18);