+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 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
package jalview.gui;\r
\r
+import jalview.datamodel.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
\r
-import jalview.datamodel.*;\r
-\r
import javax.swing.*;\r
\r
-public class IdPanel extends JPanel implements MouseListener, MouseMotionListener {\r
\r
- protected IdCanvas idCanvas;\r
- protected AlignViewport av;\r
- protected AlignmentPanel alignPanel;\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class IdPanel extends JPanel implements MouseListener,\r
+ MouseMotionListener\r
+{\r
+ protected IdCanvas idCanvas;\r
+ protected AlignViewport av;\r
+ protected AlignmentPanel alignPanel;\r
+ ScrollThread scrollThread = null;\r
+ int offy;\r
+ int width;\r
+ int lastid = -1;\r
+ boolean mouseDragging = false;\r
+\r
+ /**\r
+ * Creates a new IdPanel object.\r
+ *\r
+ * @param av DOCUMENT ME!\r
+ * @param parent DOCUMENT ME!\r
+ */\r
+ public IdPanel(AlignViewport av, AlignmentPanel parent)\r
+ {\r
+ this.av = av;\r
+ alignPanel = parent;\r
+ idCanvas = new IdCanvas(av);\r
+ setLayout(new BorderLayout());\r
+ add(idCanvas, BorderLayout.CENTER);\r
+ addMouseListener(this);\r
+ addMouseMotionListener(this);\r
+ ToolTipManager.sharedInstance().registerComponent(this);\r
+ }\r
\r
- protected int offy;\r
- public int width;\r
- public int lastid;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void mouseMoved(MouseEvent e)\r
+ {\r
+ int y = e.getY();\r
\r
+ if (av.getWrapAlignment())\r
+ {\r
+ y = getWrappedY(y);\r
+ }\r
\r
+ final int seq = av.getIndex(y);\r
+ if(seq!=-1)\r
+ {\r
+ SequenceI sequence = av.alignment.getSequenceAt(seq);\r
+ StringBuffer tip = new StringBuffer("<html>");\r
+ tip.append(sequence.getDisplayId(true));\r
+ if (av.alignment.getSequenceAt(seq).getDescription() != null)\r
+ {\r
+ tip.append("<table width=250 border=0><tr><td><i>");\r
+ tip.append(av.alignment.getSequenceAt(seq).getDescription());\r
+\r
+ //ADD NON POSITIONAL SEQUENCE INFO\r
+ SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();\r
+ if(features!=null)\r
+ {\r
+ for(int i=0; i<features.length; i++)\r
+ {\r
+ if(features[i].begin == 0 && features[i].end ==0)\r
+ {\r
+ tip.append("<br>"+features[i].featureGroup\r
+ +" "+ features[i].getType()+" "+features[i].description);\r
+ }\r
+ }\r
+ }\r
+\r
+ tip.append("</i></td></tr></table>");\r
+ }\r
+ tip.append("</html>");\r
+ setToolTipText(tip.toString());\r
+ }\r
+ }\r
\r
- boolean mouseDown;\r
- boolean mouseUp;\r
\r
- public IdPanel(AlignViewport av, AlignmentPanel parent)\r
- {\r
- this.av = av;\r
- alignPanel = parent;\r
- idCanvas = new IdCanvas(av);\r
- setLayout(new BorderLayout());\r
- add(idCanvas, BorderLayout.CENTER);\r
- addMouseListener(this);\r
- addMouseMotionListener(this);\r
- }\r
+ int getWrappedY(int y)\r
+ {\r
+ int hgap = av.charHeight;\r
+ if (av.scaleAboveWrapped)\r
+ hgap += av.charHeight;\r
\r
- public void mouseMoved(MouseEvent e) {}\r
+ return y - hgap;\r
+ }\r
\r
- public void selectSeqs(int start, int end) {\r
- if (end < start) {\r
- int tmp = start;\r
- start = end;\r
- end = tmp;\r
- }\r
\r
- for (int i = start; i <= end; i++) {\r
- SequenceI pickedSeq = av.getAlignment().getSequenceAt(i);\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void mouseDragged(MouseEvent e)\r
+ {\r
+ mouseDragging = true;\r
\r
- if (av.getSelection().contains(pickedSeq)) {\r
- av.getSelection().removeElement(pickedSeq);\r
- } else {\r
- av.getSelection().addElement(pickedSeq);\r
- }\r
- }\r
+ int y = e.getY();\r
\r
- repaint();\r
+ if (av.getWrapAlignment())\r
+ {\r
+ y = getWrappedY(y);\r
+ }\r
\r
- }\r
+ int seq = av.getIndex(y);\r
\r
- public void mouseDragged(MouseEvent e) {\r
- int y = e.getY();\r
+ if (seq < 0)\r
+ {\r
+ return;\r
+ }\r
\r
- int seq = av.getIndex(y);\r
+ if (seq < lastid)\r
+ {\r
+ selectSeqs(lastid - 1, seq);\r
+ }\r
+ else if (seq > lastid)\r
+ {\r
+ selectSeqs(lastid + 1, seq);\r
+ }\r
+\r
+ lastid = seq;\r
+ alignPanel.repaint();\r
+ }\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void mouseClicked(MouseEvent e)\r
+ {\r
+ if (e.getClickCount() < 2)\r
+ return;\r
\r
- if (mouseDown == true) {\r
- if (seq < lastid) {\r
- selectSeqs(lastid-1,seq);\r
- } else if (seq > lastid) {\r
- selectSeqs(lastid+1,seq);\r
+ java.util.Vector links = Preferences.sequenceURLLinks;\r
+ if (links == null || links.size() < 1)\r
+ return;\r
+\r
+ int y = e.getY();\r
+\r
+ if (av.getWrapAlignment())\r
+ {\r
+ y = getWrappedY(y);\r
+ }\r
+\r
+ //DEFAULT LINK IS FIRST IN THE LINK LIST\r
+ int seq = av.getIndex(y);\r
+ if(seq==-1)\r
+ return;\r
+\r
+ String id = av.getAlignment().getSequenceAt(seq).getName();\r
+ if (id.indexOf("|") > -1)\r
+ id = id.substring(id.lastIndexOf("|") + 1);\r
+\r
+\r
+ String url = links.elementAt(0).toString();\r
+ url = url.substring(url.indexOf("|")+1);\r
+\r
+ int index = url.indexOf("$SEQUENCE_ID$");\r
+ url = url.substring(0, index)+ id + url.substring(index+13);\r
+\r
+ try\r
+ {\r
+ jalview.util.BrowserLauncher.openURL(url);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Unixers: Couldn't find default web browser."\r
+ +"\nAdd the full path to your browser in Preferences.",\r
+ "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
+ ex.printStackTrace();\r
}\r
- lastid = seq;\r
}\r
\r
- return;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void mouseEntered(MouseEvent e)\r
+ {\r
+ if (scrollThread != null)\r
+ {\r
+ scrollThread.running = false;\r
+ }\r
+ }\r
\r
- public void mouseClicked(MouseEvent e)\r
- {\r
- if (e.getClickCount() == 2)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void mouseExited(MouseEvent e)\r
{\r
- int seq = av.getIndex(e.getY());\r
- String id = av.getAlignment().getSequenceAt(seq).getName();\r
-\r
- try{\r
- jalview.util.BrowserLauncher.openURL(\r
- "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" + id +\r
- "]+-vn+2");\r
- }catch(Exception ex){ex.printStackTrace();}\r
+ if (av.getWrapAlignment())\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))\r
+ {\r
+ scrollThread = new ScrollThread(true);\r
+ }\r
+\r
+ if (mouseDragging && (e.getY() >= getHeight()) &&\r
+ (av.alignment.getHeight() > av.getEndSeq()))\r
+ {\r
+ scrollThread = new ScrollThread(false);\r
+ }\r
}\r
\r
- }\r
- public void mouseEntered(MouseEvent e) { }\r
- public void mouseExited (MouseEvent e) { }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void mousePressed(MouseEvent e)\r
+ {\r
+ if (e.getClickCount() == 2)\r
+ {\r
+ return;\r
+ }\r
\r
- public void mousePressed(MouseEvent e) {\r
- if (e.getClickCount() == 2)\r
- return;\r
+ int y = e.getY();\r
\r
- int y = e.getY();\r
- int seq = av.getIndex(y);\r
+ if (av.getWrapAlignment())\r
+ {\r
+ y = getWrappedY(y);\r
+ }\r
\r
- mouseDown = true;\r
+ int seq = av.getIndex(y);\r
\r
- if( javax.swing.SwingUtilities.isRightMouseButton(e))\r
- {\r
- String id = av.getAlignment().getSequenceAt(seq).getName();\r
- String s = (String)JOptionPane.showInternalInputDialog(\r
- this,\r
- "Edit sequence name",\r
- "Edit sequence name",\r
- JOptionPane.PLAIN_MESSAGE,\r
- null,\r
- null,\r
- id);\r
+ if (seq == -1)\r
+ {\r
+ return;\r
+ }\r
\r
- if(s!=null)\r
+ if (javax.swing.SwingUtilities.isRightMouseButton(e))\r
{\r
- av.getAlignment().getSequenceAt(seq).setName(s);\r
- alignPanel.RefreshPanels();\r
+ jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,\r
+ (Sequence) av.getAlignment().getSequenceAt(seq),\r
+ Preferences.sequenceURLLinks);\r
+ pop.show(this, e.getX(), y);\r
+\r
+ return;\r
}\r
\r
- }\r
- else\r
- {\r
- if (seq != -1)\r
- selectSeqs(seq,seq);\r
+ /* if (!e.isControlDown() && !e.isShiftDown() &&\r
+ (av.alignment.findGroup(av.alignment.getSequenceAt(seq)) != null))\r
+ {\r
+ System.out.println("no modifiers");\r
+ SequenceGroup selection = new SequenceGroup();\r
+ SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(\r
+ seq));\r
+ selection.setStartRes(0);\r
+ selection.setEndRes(av.alignment.getWidth() - 1);\r
+\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ selection.addSequence(sg.getSequenceAt(i), true);\r
+ }\r
+\r
+ av.setSelectionGroup(selection);\r
+\r
+ return;\r
+ }*/\r
+\r
+ if ((av.getSelectionGroup() == null) ||\r
+ ((!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null))\r
+ {\r
+ av.setSelectionGroup(new SequenceGroup());\r
+ av.getSelectionGroup().setStartRes(0);\r
+ av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);\r
+ }\r
+\r
+\r
\r
+ if (e.isShiftDown() && (lastid != -1))\r
+ {\r
+ selectSeqs(lastid, seq);\r
+ }\r
+ else\r
+ {\r
+ selectSeq(seq);\r
+ }\r
+\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param seq DOCUMENT ME!\r
+ */\r
+ void selectSeq(int seq)\r
+ {\r
lastid = seq;\r
- }\r
- return;\r
- }\r
\r
- public void mouseReleased(MouseEvent e) {\r
- lastid = -1;\r
+ SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);\r
+ av.getSelectionGroup().addOrRemove(pickedSeq, true);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param start DOCUMENT ME!\r
+ * @param end DOCUMENT ME!\r
+ */\r
+ void selectSeqs(int start, int end)\r
+ {\r
+ if(av.getSelectionGroup()==null)\r
+ return;\r
+\r
+ lastid = start;\r
+\r
+ if (end < start)\r
+ {\r
+ int tmp = start;\r
+ start = end;\r
+ end = tmp;\r
+ lastid = end;\r
+ }\r
+\r
+ for (int i = start; i <= end; i++)\r
+ {\r
+ av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),\r
+ true);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void mouseReleased(MouseEvent e)\r
+ {\r
+ if (scrollThread != null)\r
+ {\r
+ scrollThread.running = false;\r
+ }\r
+\r
+ mouseDragging = false;\r
+ PaintRefresher.Refresh(av.alignment);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param found DOCUMENT ME!\r
+ */\r
+ public void highlightSearchResults(java.util.Vector found)\r
+ {\r
+ idCanvas.setHighlighted(found);\r
+\r
+ if (found == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ int index = av.alignment.findIndex((SequenceI) found.get(0));\r
\r
- mouseDown = false;\r
- mouseUp = true;\r
+ // do we need to scroll the panel?\r
+ if ((av.getStartSeq() > index) || (av.getEndSeq() < index))\r
+ {\r
+ alignPanel.setScrollValues(av.getStartRes(), index);\r
+ }\r
+ }\r
\r
- PaintRefresher.Refresh(this);\r
+ // this class allows scrolling off the bottom of the visible alignment\r
+ class ScrollThread extends Thread\r
+ {\r
+ boolean running = false;\r
+ boolean up = true;\r
\r
- }\r
+ public ScrollThread(boolean up)\r
+ {\r
+ this.up = up;\r
+ start();\r
+ }\r
+\r
+ public void stopScrolling()\r
+ {\r
+ running = false;\r
+ }\r
+\r
+ public void run()\r
+ {\r
+ running = true;\r
+\r
+ while (running)\r
+ {\r
+ if (alignPanel.scrollUp(up))\r
+ {\r
+ // scroll was ok, so add new sequence to selection\r
+ int seq = av.getStartSeq();\r
+\r
+ if (!up)\r
+ {\r
+ seq = av.getEndSeq();\r
+ }\r
+\r
+ if (seq < lastid)\r
+ {\r
+ selectSeqs(lastid - 1, seq);\r
+ }\r
+ else if (seq > lastid)\r
+ {\r
+ selectSeqs(lastid + 1, seq);\r
+ }\r
+\r
+ lastid = seq;\r
+ }\r
+ else\r
+ {\r
+ running = false;\r
+ }\r
+\r
+ alignPanel.repaint();\r
+\r
+ try\r
+ {\r
+ Thread.sleep(100);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+ }\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff