X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=63d7c532a593e9d670187b956323d145710ed2b2;hb=d545553b53ac1bd1e29eb72250cdb29745f7292f;hp=560c9839d4f9bf19d921fb727a53405235d444f7;hpb=dd6a434e05eef33808d4cda23dd2c6f8d10a4630;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 560c983..63d7c53 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -1,440 +1,602 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 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 - */ -package jalview.gui; - -import jalview.datamodel.*; - -import java.awt.*; -import java.awt.event.*; -import java.awt.image.*; - -import javax.swing.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class AnnotationLabels extends JPanel implements MouseListener, - MouseMotionListener, ActionListener -{ - static String ADDNEW = "Add New Row"; - static String HIDE = "Hide This Row"; - static String DELETE = "Delete This Row"; - static String SHOWALL = "Show All Hidden Rows"; - static String OUTPUT_TEXT = "Show Values In Textbox"; - boolean active = false; - Image image; - AlignmentPanel ap; - AlignViewport av; - boolean resizing = false; - int oldY; - int mouseX; - int selectedRow = 0; - int scrollOffset = 0; - Font font = new Font("Arial", Font.PLAIN, 11); - - - /** - * Creates a new AnnotationLabels object. - * - * @param ap DOCUMENT ME! - */ - public AnnotationLabels(AlignmentPanel ap) - { - this.ap = ap; - av = ap.av; - - java.net.URL url = getClass().getResource("/images/idwidth.gif"); - Image temp = null; - - if (url != null) - { - temp = java.awt.Toolkit.getDefaultToolkit().createImage(url); - } - - try - { - MediaTracker mt = new MediaTracker(this); - mt.addImage(temp, 0); - mt.waitForID(0); - } - catch (Exception ex) - { - } - - 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); - image = (Image) bi; - - addMouseListener(this); - addMouseMotionListener(this); - } - - public AnnotationLabels(AlignViewport av) - { - this.av = av; - } - - /** - * DOCUMENT ME! - * - * @param y DOCUMENT ME! - */ - public void setScrollOffset(int y) - { - scrollOffset = y; - repaint(); - } - - /** - * 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)) - { - String label = JOptionPane.showInputDialog(this, - "Label for annotation"); - - if (label == null) - { - label = ""; - } - - ap.av.alignment.addAnnotation(new AlignmentAnnotation(label, - "New description", - new Annotation[ap.av.alignment.getWidth()])); - - dif = aa[aa.length - 1].height; - } - else if (evt.getActionCommand().equals(HIDE)) - { - aa[selectedRow].visible = false; - - if (aa[selectedRow].label.equals("Conservation")) - { - ap.av.showConservation = false; - } - - if (aa[selectedRow].label.equals("Quality")) - { - ap.av.showQuality = false; - } - - if (aa[selectedRow].label.equals("Consensus")) - { - ap.av.showIdentity = false; - } - - 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) - { - dif += aa[i].height; - aa[i].visible = true; - } - } - } - else if (evt.getActionCommand().equals(OUTPUT_TEXT)) - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - Desktop.addInternalFrame(cap, - ap.alignFrame.getTitle() + " - " + aa[selectedRow].label, 500, - 100); - cap.setText(aa[selectedRow].toString()); - } - - - ap.annotationPanel.adjustPanelHeight(); - - Dimension d = ap.annotationScroller.getPreferredSize(); - ap.annotationScroller.setPreferredSize(new Dimension(d.width, - d.height + dif)); - d = ap.annotationSpaceFillerHolder.getPreferredSize(); - ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(d.width, - d.height + dif)); - - ap.addNotify(); - } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mousePressed(MouseEvent evt) - { - oldY = evt.getY(); - } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseReleased(MouseEvent evt) - { - active = false; - repaint(); - } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseEntered(MouseEvent evt) - { - active = true; - repaint(); - } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseExited(MouseEvent evt) - { - active = false; - repaint(); - } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseDragged(MouseEvent evt) - { - active = true; - - Dimension d = ap.annotationScroller.getPreferredSize(); - int dif = evt.getY() - oldY; - - dif /= ap.av.charHeight; - dif *= ap.av.charHeight; - - if ((d.height - dif) > 20) - { - ap.annotationScroller.setPreferredSize(new Dimension(d.width, - d.height - dif)); - d = ap.annotationSpaceFillerHolder.getPreferredSize(); - ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension( - d.width, d.height - dif)); - ap.repaint(); - } - - ap.addNotify(); - } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseMoved(MouseEvent evt) - { - } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseClicked(MouseEvent evt) - { - int y = evt.getY() - scrollOffset; - 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); - pop.add(item); - pop.show(this, evt.getX(), evt.getY()); - - return; - } - - int height = 0; - - for (int i = 0; i < aa.length; i++) - { - if (!aa[i].visible) - { - continue; - } - - height += aa[i].height; - - if (y < height) - { - selectedRow = i; - - break; - } - } - - JPopupMenu pop = new JPopupMenu("Annotations"); - JMenuItem item = new JMenuItem(ADDNEW); - item.addActionListener(this); - pop.add(item); - item = new JMenuItem(HIDE); - item.addActionListener(this); - pop.add(item); - item = new JMenuItem(DELETE); - item.addActionListener(this); - pop.add(item); - item = new JMenuItem(SHOWALL); - item.addActionListener(this); - pop.add(item); - item = new JMenuItem(OUTPUT_TEXT); - item.addActionListener(this); - pop.add(item); - - if (aa[selectedRow].label.equals("Consensus")) - { - pop.addSeparator(); - final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( - "Ignore Gaps In Consensus", - ap.av.getIgnoreGapsConsensus()); - cbmi.addActionListener(new ActionListener() - {public void actionPerformed(ActionEvent e) - { - ap.av.setIgnoreGapsConsensus(cbmi.getState()); - ap.repaint(); - } - }); - pop.add(cbmi); - - } - - pop.show(this, evt.getX(), evt.getY()); - } - - /** - * DOCUMENT ME! - * - * @param g1 DOCUMENT ME! - */ - public void paintComponent(Graphics g) - { - - int width = getWidth(); - if(width==0) - width = ap.calculateIdWidth().width + 4; - - Graphics2D g2 = (Graphics2D) g; - g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); - - drawComponent(g2, width); - - } - - /** - * DOCUMENT ME! - * - * @param g DOCUMENT ME! - */ - public void drawComponent(Graphics g, int width) - { - if(av.getFont().getSize()<10) - g.setFont(new Font("Arial", Font.PLAIN, av.getFont().getSize()-1)); - else - g.setFont(font); - - FontMetrics fm = g.getFontMetrics(g.getFont()); - g.setColor(Color.white); - g.fillRect(0, 0, getWidth(), getHeight()); - - g.translate(0, scrollOffset); - g.setColor(Color.black); - - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - int y = g.getFont().getSize(); - int x = 0; - - - if (aa != null) - { - for (int i = 0; i < aa.length; i++) - { - if (!aa[i].visible) - { - continue; - } - - x = width - fm.stringWidth(aa[i].label) - 3; - - if (aa[i].graph>0) - { - y += (aa[i].height / 3); - } - - g.drawString(aa[i].label, x, y); - - if (aa[i].graph>0) - { - y += ((2 * aa[i].height) / 3); - } - else - { - y += aa[i].height; - } - } - } - - if (active) - { - if (image != null) - { - g.drawImage(image, 2, 0, this); - } - } - - if ((aa == null) || (aa.length < 1)) - { - g.drawString("Right click", 2, 8); - g.drawString("to add annotation", 2, 18); - } - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2006 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 + */ +package jalview.gui; + +import jalview.datamodel.*; +import jalview.io.FormatAdapter; + +import java.awt.*; +import java.awt.datatransfer.StringSelection; +import java.awt.event.*; +import java.awt.image.*; +import java.util.Vector; + +import javax.swing.*; + + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class AnnotationLabels extends JPanel implements MouseListener, + MouseMotionListener, ActionListener +{ + static String ADDNEW = "Add New Row"; + 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! + */ + public AnnotationLabels(AlignmentPanel ap) + { + this.ap = ap; + av = ap.av; + + java.net.URL url = getClass().getResource("/images/idwidth.gif"); + Image temp = null; + + if (url != null) + { + temp = java.awt.Toolkit.getDefaultToolkit().createImage(url); + } + + try + { + MediaTracker mt = new MediaTracker(this); + mt.addImage(temp, 0); + mt.waitForID(0); + } + catch (Exception ex) + { + } + + 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); + image = (Image) bi; + + addMouseListener(this); + addMouseMotionListener(this); + } + + public AnnotationLabels(AlignViewport av) + { + this.av = av; + } + + /** + * DOCUMENT ME! + * + * @param y DOCUMENT ME! + */ + public void setScrollOffset(int y) + { + scrollOffset = y; + repaint(); + } + + void getSelectedRow(int y) + { + int height = 0; + AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + + if(aa!=null) + { + for (int i = 0; i < aa.length; i++) + { + if (!aa[i].visible) + { + continue; + } + + height += aa[i].height; + + if (y < height) + { + selectedRow = i; + + break; + } + } + } + } + + /** + * 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)) + { + String label = JOptionPane.showInputDialog(this, + "Label for annotation"); + + if (label == null) + { + label = ""; + } + + AlignmentAnnotation newAnnotation = new AlignmentAnnotation(label, + "New description", + new Annotation[ap.av.alignment.getWidth()]); + + 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(HIDE)) + { + aa[selectedRow].visible = false; + + if (aa[selectedRow].label.equals("Conservation")) + { + ap.av.showConservation = false; + } + + if (aa[selectedRow].label.equals("Quality")) + { + ap.av.showQuality = false; + } + + if (aa[selectedRow].label.equals("Consensus")) + { + ap.av.showIdentity = false; + } + + 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) + { + dif += aa[i].height; + aa[i].visible = true; + } + } + } + else if (evt.getActionCommand().equals(OUTPUT_TEXT)) + { + new AnnotationExporter().exportAnnotations( + ap, + new AlignmentAnnotation[] + {aa[selectedRow]} + ); + } + else if (evt.getActionCommand().equals(COPYCONS_SEQ)) + { + SequenceI cons=av.getConsensusSeq(); + if (cons!=null) + copy_annotseqtoclipboard(cons); + + } + + ap.annotationPanel.adjustPanelHeight(); + ap.annotationScroller.validate(); + ap.repaint(); + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mousePressed(MouseEvent evt) + { + getSelectedRow(evt.getY() - scrollOffset); + oldY = evt.getY(); + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseReleased(MouseEvent evt) + { + int start = selectedRow; + getSelectedRow(evt.getY() - scrollOffset); + int end = selectedRow; + + if(start!=end) + { + //Swap these annotations + AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[start]; + AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end]; + + + ap.av.alignment.getAlignmentAnnotation()[end] = startAA; + ap.av.alignment.getAlignmentAnnotation()[start] = endAA; + } + + resizePanel = false; + dragEvent = null; + repaint(); + ap.annotationPanel.repaint(); + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseEntered(MouseEvent evt) + { + if(evt.getY()<10) + { + resizePanel = true; + repaint(); + } + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseExited(MouseEvent evt) + { + if(dragEvent == null) + { + resizePanel = false; + repaint(); + } + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseDragged(MouseEvent evt) + { + dragEvent = evt; + + if (resizePanel) + { + Dimension d = ap.annotationScroller.getPreferredSize(); + int dif = evt.getY() - oldY; + + dif /= ap.av.charHeight; + dif *= ap.av.charHeight; + + if ( (d.height - dif) > 20) + { + ap.annotationScroller.setPreferredSize(new Dimension(d.width, + d.height - dif)); + d = ap.annotationSpaceFillerHolder.getPreferredSize(); + ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension( + d.width, d.height - dif)); + ap.repaint(); + } + + ap.addNotify(); + } + else + repaint(); + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseMoved(MouseEvent evt) + { + resizePanel = evt.getY()<10; + + repaint(); + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseClicked(MouseEvent evt) + { + if(!SwingUtilities.isRightMouseButton(evt)) + return; + + 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); + 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(HIDE); + item.addActionListener(this); + pop.add(item); + item = new JMenuItem(DELETE); + item.addActionListener(this); + pop.add(item); + 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 (aa[selectedRow].label.equals("Consensus")) + { + pop.addSeparator(); + final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( + "Ignore Gaps In Consensus", + ap.av.getIgnoreGapsConsensus()); + cbmi.addActionListener(new ActionListener() + {public void actionPerformed(ActionEvent e) + { + ap.av.setIgnoreGapsConsensus(cbmi.getState()); + ap.repaint(); + } + }); + pop.add(cbmi); + final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); + consclipbrd.addActionListener(this); + pop.add(consclipbrd); + } + + pop.show(this, evt.getX(), evt.getY()); + } + /** + * do a single sequence copy to jalview and the system clipboard + * + * @param sq sequence to be copied to clipboard + */ + protected void copy_annotseqtoclipboard(SequenceI sq) + { + SequenceI [] seqs = new SequenceI[] { sq }; + String[] omitHidden = null; + SequenceI [] dseqs=new SequenceI[] { sq.getDatasetSequence()}; + if (dseqs[0]==null) { + dseqs[0] = new Sequence(sq); + dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sq.getSequence())); + sq.setDatasetSequence(dseqs[0]); + } + Alignment ds=new Alignment(dseqs); + if (av.hasHiddenColumns) + { + omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, sq.getLength(), seqs); + } + + String output = new FormatAdapter().formatSequences( + "Fasta", + seqs, + omitHidden); + + + Toolkit.getDefaultToolkit().getSystemClipboard() + .setContents(new StringSelection(output), Desktop.instance); + + Vector hiddenColumns = null; + if(av.hasHiddenColumns) + { + hiddenColumns =new Vector(); + for(int i=0; i0 && aa[i].graphHeight>0) + { + graphExtras = y; + + y += (aa[i].height / 3); + + if(aa[i].graphGroup<0) + graphExtras = y + fontHeight; + } + + if(aa[i].graphGroup>-1) + { + int groupSize = 0; + for (int gg = 0; gg < aa.length; gg++) + { + if (aa[gg].graphGroup == aa[i].graphGroup) + groupSize++; + } + + if(groupSize * (fontHeight+8) < aa[i].height) + graphExtras += (aa[i].height -( groupSize * (fontHeight+8)) )/2; + + for(int gg=0; gg0) + { + /* 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; + } + } + } + + if (resizePanel) + { + g.drawImage(image, 2, 0 - scrollOffset, this); + } + else if (dragEvent != null && aa!=null) + { + g.setColor(Color.lightGray); + g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent.getY() - scrollOffset); + } + + + if ((aa == null) || (aa.length < 1)) + { + g.drawString("Right click", 2, 8); + g.drawString("to add annotation", 2, 18); + } + } +}