-/*
- * 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.appletgui;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.util.Vector;
-
-import jalview.datamodel.*;
-
-public class AnnotationLabels
- extends Panel implements ActionListener
-{
- boolean active = false;
- AlignmentPanel ap;
- AlignViewport av;
- boolean resizing = false;
- int oldY, mouseX;
- 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";
- static String COPYCONS_SEQ = "Copy Consensus Sequence";
-
- int selectedRow = 0;
- int scrollOffset = 0;
-
- public AnnotationLabels(AlignmentPanel ap)
- {
- this.ap = ap;
- this.av = ap.av;
- setLayout(null);
- addMouseListener(new MouseAdapter()
- {
- public void mousePressed(MouseEvent evt)
- {
- doMousePressed(evt);
- }
- });
- }
-
- public AnnotationLabels(AlignViewport av)
-{
- this.av = av;
-}
-
-
- public void setScrollOffset(int y)
- {
- scrollOffset = y;
- repaint();
- }
-
- public void actionPerformed(ActionEvent evt)
- {
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-
- if (evt.getActionCommand().equals(HIDE))
- {
- aa[selectedRow].visible = false;
- }
- else if (evt.getActionCommand().equals(SHOWALL))
- {
- for (int i = 0; i < aa.length; i++)
- {
- aa[i].visible = true;
- }
- }
- else if (evt.getActionCommand().equals(OUTPUT_TEXT))
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame,
- ap.alignFrame.getTitle() + " - " +
- aa[selectedRow].label, 500, 100);
- cap.setText(aa[selectedRow].toString());
- }
- else if (evt.getActionCommand().equals(COPYCONS_SEQ))
- {
- SequenceI cons=av.getConsensusSeq();
- if (cons!=null)
- copy_annotseqtoclipboard(cons);
-
- }
- ap.annotationPanel.adjustPanelHeight();
- setSize(getSize().width, ap.annotationPanel.getSize().height);
- ap.validate();
- ap.repaint();
- }
-
- public void doMousePressed(MouseEvent evt)
- {
- int y = evt.getY() - scrollOffset;
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
- 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;
- }
- }
-
- PopupMenu pop = new PopupMenu("Annotations");
- MenuItem item = new MenuItem(HIDE);
- item.addActionListener(this);
- pop.add(item);
- item = new MenuItem(SHOWALL);
- item.addActionListener(this);
- pop.add(item);
- this.add(pop);
- item = new MenuItem(OUTPUT_TEXT);
- item.addActionListener(this);
- pop.add(item);
-
- if (aa[selectedRow].label.equals("Consensus"))
- {
- pop.addSeparator();
- final CheckboxMenuItem cbmi = new CheckboxMenuItem(
- "Ignore Gaps In Consensus",
- ap.av.getIgnoreGapsConsensus());
-
- cbmi.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent e)
- {
- ap.av.setIgnoreGapsConsensus(cbmi.getState());
- ap.repaint();
- }
- });
- pop.add(cbmi);
- final MenuItem cpcons=new MenuItem(COPYCONS_SEQ);
- cpcons.addActionListener(this);
- pop.add(cpcons);
- }
-
- pop.show(this, evt.getX(), evt.getY());
-
- }
-/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- protected void copy_annotseqtoclipboard(SequenceI sq)
- {
- if (sq==null || sq.getLength()<1)
- return;
- jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
- jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t" +
- sq.getStart() + "\t" +
- sq.getEnd() + "\t" +
- sq.getSequence() + "\n");
- if (av.hasHiddenColumns)
- {
- jalview.appletgui.AlignFrame.copiedHiddenColumns=new Vector();
- for(int i=0; i<av.getColumnSelection().getHiddenColumns().size(); i++)
- {
- int[] region = (int[])
- av.getColumnSelection().getHiddenColumns().elementAt(i);
-
- jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement(new int[]{region[0],
- region[1]});
- }
- }
- }
-
- public void paint(Graphics g)
- {
- drawComponent(g, getSize().width);
- }
-
- public void drawComponent(Graphics g, int width)
- {
- g.setFont(av.getFont());
- FontMetrics fm = g.getFontMetrics(av.getFont());
- g.setColor(Color.white);
- g.fillRect(0, 0, getSize().width, getSize().height);
-
- 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;
- }
- }
- }
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
+\r
+package jalview.appletgui;\r
+\r
+import java.util.*;\r
+\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+\r
+import jalview.datamodel.*;\r
+\r
+public class AnnotationLabels\r
+ extends Panel implements ActionListener, MouseListener, MouseMotionListener\r
+{\r
+ Image image;\r
+ boolean active = false;\r
+ AlignmentPanel ap;\r
+ AlignViewport av;\r
+ boolean resizing = false;\r
+ int oldY, mouseX;\r
+ static String EDITNAME = "Edit label/description";\r
+ static String HIDE = "Hide this row";\r
+ static String DELETE = "Delete this row";\r
+ static String SHOWALL = "Show all hidden rows";\r
+ static String OUTPUT_TEXT = "Show Values In Textbox";\r
+ static String COPYCONS_SEQ = "Copy Consensus Sequence";\r
+\r
+ int selectedRow = 0;\r
+ int scrollOffset = 0;\r
+\r
+ Tooltip tooltip;\r
+\r
+ public AnnotationLabels(AlignmentPanel ap)\r
+ {\r
+ this.ap = ap;\r
+ this.av = ap.av;\r
+ setLayout(null);\r
+ addMouseListener(this);\r
+ addMouseMotionListener(this);\r
+ }\r
+\r
+ public AnnotationLabels(AlignViewport av)\r
+ {\r
+ this.av = av;\r
+ }\r
+\r
+ public void setScrollOffset(int y)\r
+ {\r
+ scrollOffset = y;\r
+ repaint();\r
+ }\r
+\r
+ void getSelectedRow(int y)\r
+ {\r
+ selectedRow = -1;\r
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
+\r
+ if (aa == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ int height = 0;\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if (!aa[i].visible)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ height += aa[i].height;\r
+ if (y < height)\r
+ {\r
+ selectedRow = i;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+\r
+ if (evt.getActionCommand().equals(EDITNAME))\r
+ {\r
+ EditNameDialog dialog = new EditNameDialog(\r
+ aa[selectedRow].label,\r
+ aa[selectedRow].description,\r
+ " Annotation Label",\r
+ "Annotation Description",\r
+ ap,\r
+ "Edit Annotation Name / Description");\r
+\r
+ if (dialog.accept)\r
+ {\r
+ aa[selectedRow].label = dialog.getName();\r
+ aa[selectedRow].description = dialog.getDescription();\r
+ repaint();\r
+ }\r
+ }\r
+ if (evt.getActionCommand().equals(HIDE))\r
+ {\r
+ aa[selectedRow].visible = false;\r
+ }\r
+ else if (evt.getActionCommand().equals(SHOWALL))\r
+ {\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ aa[i].visible = true;\r
+ }\r
+ }\r
+ else if (evt.getActionCommand().equals(OUTPUT_TEXT))\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame,\r
+ ap.alignFrame.getTitle() + " - " +\r
+ aa[selectedRow].label, 500, 100);\r
+ cap.setText(aa[selectedRow].toString());\r
+ }\r
+ else if (evt.getActionCommand().equals(COPYCONS_SEQ))\r
+ {\r
+ SequenceI cons = av.getConsensusSeq();\r
+ if (cons != null)\r
+ {\r
+ copy_annotseqtoclipboard(cons);\r
+ }\r
+\r
+ }\r
+ ap.annotationPanel.adjustPanelHeight();\r
+ setSize(getSize().width, ap.annotationPanel.getSize().height);\r
+ ap.validate();\r
+ ap.repaint();\r
+ }\r
+\r
+ public void mouseMoved(MouseEvent evt)\r
+ {\r
+ getSelectedRow(evt.getY() - scrollOffset);\r
+\r
+ if (selectedRow > -1)\r
+ {\r
+ if (tooltip == null)\r
+ {\r
+ tooltip = new Tooltip(ap.av.alignment.\r
+ getAlignmentAnnotation()[selectedRow].\r
+ description,\r
+ this);\r
+ }\r
+ else\r
+ {\r
+ tooltip.setTip(ap.av.alignment.\r
+ getAlignmentAnnotation()[selectedRow].description);\r
+ }\r
+ }\r
+ else if (tooltip != null)\r
+ {\r
+ tooltip.setTip("");\r
+ }\r
+\r
+ }\r
+\r
+ public void mouseDragged(MouseEvent evt)\r
+ {}\r
+\r
+ public void mouseClicked(MouseEvent evt)\r
+ {}\r
+\r
+ public void mouseReleased(MouseEvent evt)\r
+ {}\r
+\r
+ public void mouseEntered(MouseEvent evt)\r
+ {}\r
+\r
+ public void mouseExited(MouseEvent evt)\r
+ {}\r
+\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
+\r
+ PopupMenu pop = new PopupMenu("Annotations");\r
+\r
+ MenuItem item = new MenuItem(EDITNAME);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new MenuItem(HIDE);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new MenuItem(SHOWALL);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ this.add(pop);\r
+ item = new MenuItem(OUTPUT_TEXT);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+\r
+ if (aa[selectedRow] == ap.av.consensus)\r
+ {\r
+ pop.addSeparator();\r
+ final CheckboxMenuItem cbmi = new CheckboxMenuItem(\r
+ "Ignore Gaps In Consensus",\r
+ ap.av.getIgnoreGapsConsensus());\r
+\r
+ cbmi.addItemListener(new ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent e)\r
+ {\r
+ ap.av.setIgnoreGapsConsensus(cbmi.getState());\r
+ ap.repaint();\r
+ }\r
+ });\r
+ pop.add(cbmi);\r
+ final MenuItem cpcons = new MenuItem(COPYCONS_SEQ);\r
+ cpcons.addActionListener(this);\r
+ pop.add(cpcons);\r
+ }\r
+\r
+ pop.show(this, evt.getX(), evt.getY());\r
+\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void copy_annotseqtoclipboard(SequenceI sq)\r
+ {\r
+ if (sq == null || sq.getLength() < 1)\r
+ {\r
+ return;\r
+ }\r
+ jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();\r
+ jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t" +\r
+ sq.getStart() + "\t" +\r
+ sq.getEnd() + "\t" +\r
+ sq.getSequenceAsString() + "\n");\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();\r
+ for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)\r
+ {\r
+ int[] region = (int[])\r
+ av.getColumnSelection().getHiddenColumns().elementAt(i);\r
+\r
+ jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement(new int[]\r
+ {region[0],\r
+ region[1]});\r
+ }\r
+ }\r
+ }\r
+\r
+ public void update(Graphics g)\r
+ {\r
+ paint(g);\r
+ }\r
+\r
+ public void paint(Graphics g)\r
+ {\r
+ int w = getSize().width;\r
+ if (image == null || w != image.getWidth(this))\r
+ {\r
+ image = createImage(w, ap.annotationPanel.getSize().height);\r
+ }\r
+\r
+ drawComponent(image.getGraphics(), w);\r
+ g.drawImage(image, 0, 0, this);\r
+ }\r
+\r
+ public void drawComponent(Graphics g, int width)\r
+ {\r
+ g.setFont(av.getFont());\r
+ FontMetrics fm = g.getFontMetrics(av.getFont());\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
+\r
+ g.translate(0, scrollOffset);\r
+ g.setColor(Color.black);\r
+\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ int y = g.getFont().getSize();\r
+ int x = 0;\r
+\r
+ if (aa != null)\r
+ {\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if (!aa[i].visible)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ x = width - fm.stringWidth(aa[i].label) - 3;\r
+\r
+ if (aa[i].graph > 0)\r
+ {\r
+ y += (aa[i].height / 3);\r
+ }\r
+\r
+ g.drawString(aa[i].label, x, y);\r
+\r
+ if (aa[i].graph > 0)\r
+ {\r
+ y += (2 * aa[i].height / 3);\r
+ }\r
+ else\r
+ {\r
+ y += aa[i].height;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+}\r
git://source.jalview.org / jalview.git / blobdiff