-package jalview.appletgui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class IdPanel extends Panel implements MouseListener, MouseMotionListener {\r
-\r
- protected IdCanvas idCanvas;\r
- protected AlignViewport av;\r
- protected AlignmentPanel alignPanel;\r
- ScrollThread scrollThread = null;\r
-\r
- int offy;\r
- int width;\r
- int lastid = -1;\r
- boolean mouseDragging = false;\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
- idCanvas.addMouseListener(this);\r
- idCanvas.addMouseMotionListener(this);\r
- }\r
-\r
- public void mouseMoved(MouseEvent e) {}\r
-\r
-\r
- public void mouseDragged(MouseEvent e) {\r
- mouseDragging = true;\r
-\r
- int y = e.getY();\r
- if(av.getWrapAlignment())\r
- y-=2*av.charHeight;\r
- int seq = av.getIndex(y);\r
-\r
- if(seq<0)\r
- return;\r
-\r
- if (seq < lastid)\r
- selectSeqs(lastid - 1, seq);\r
- else if (seq > lastid)\r
- selectSeqs(lastid + 1, seq);\r
-\r
- lastid = seq;\r
- alignPanel.repaint();\r
- }\r
-\r
- public void mouseClicked(MouseEvent e)\r
- {\r
- if (e.getClickCount() == 2)\r
- {\r
- int y = e.getY();\r
- if(av.getWrapAlignment())\r
- y-=2*av.charHeight;\r
-\r
- int seq = av.getIndex(y);\r
- String id = av.getAlignment().getSequenceAt(seq).getName();\r
-\r
- try{\r
- jalview.bin.JalviewLite.showURL(\r
- "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" + id +\r
- "]+-vn+2");\r
- }catch(Exception ex){ex.printStackTrace();}\r
- }\r
-\r
- }\r
- public void mouseEntered(MouseEvent e)\r
- {\r
- if(scrollThread!=null)\r
- scrollThread.running = false;\r
- }\r
-\r
- public void mouseExited (MouseEvent e)\r
- {\r
- if(av.getWrapAlignment())\r
- return;\r
-\r
- if(mouseDragging && e.getY()<0 && av.getStartSeq()>0)\r
- {\r
- scrollThread = new ScrollThread(true);\r
- }\r
-\r
- if(mouseDragging && e.getY()>=getSize().height && av.alignment.getHeight()>av.getEndSeq())\r
- {\r
- scrollThread = new ScrollThread(false);\r
- }\r
- }\r
-\r
-\r
- public void mousePressed(MouseEvent e) {\r
- if (e.getClickCount() == 2)\r
- return;\r
-\r
- int y = e.getY();\r
- if(av.getWrapAlignment())\r
- y-=2*av.charHeight;\r
-\r
- int seq = av.getIndex(y);\r
- if (seq == -1)\r
- return;\r
-\r
- if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)\r
- {\r
- APopupMenu popup = new APopupMenu(alignPanel, null);\r
- this.add(popup);\r
- popup.show(this, e.getX(), e.getY());\r
- return;\r
- }\r
-\r
-\r
- if(!e.isControlDown() && !e.isShiftDown() && av.alignment.findGroup( av.alignment.getSequenceAt(seq))!=null)\r
- {\r
-\r
- SequenceGroup selection = new SequenceGroup();\r
- SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(seq));\r
- selection.setStartRes(0);\r
- selection.setEndRes(av.alignment.getWidth()-1);\r
- for (int i =0; i< sg.getSize(); i++)\r
- selection.addSequence(sg.getSequenceAt(i));\r
-\r
- av.setSelectionGroup(selection);\r
- return;\r
- }\r
-\r
- if(av.getSelectionGroup()==null || ( !e.isControlDown() && av.getSelectionGroup()!=null))\r
- av.setSelectionGroup(new SequenceGroup());\r
-\r
- av.getSelectionGroup().setStartRes(0);\r
- av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1);\r
-\r
- if(e.isShiftDown() && lastid!=-1)\r
- selectSeqs(lastid, seq);\r
- else\r
- selectSeq(seq);\r
-\r
- alignPanel.repaint();\r
- }\r
-\r
- void selectSeq(int seq)\r
- {\r
- lastid = seq;\r
- SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);\r
- av.getSelectionGroup().addOrRemove(pickedSeq);\r
- }\r
-\r
- void selectSeqs(int start, int end) {\r
-\r
- lastid = start;\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
- av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i));\r
-\r
- }\r
-\r
-\r
- public void mouseReleased(MouseEvent e)\r
- {\r
- if(scrollThread!=null)\r
- scrollThread.running = false;\r
-\r
- mouseDragging = false;\r
- PaintRefresher.Refresh(this);\r
- }\r
-\r
- public void highlightSearchResults( java.util.Vector found )\r
- {\r
- idCanvas.setHighlighted( found );\r
-\r
- if(found == null)\r
- return;\r
-\r
- int index = av.alignment.findIndex( (SequenceI)found.elementAt(0));\r
-\r
- // do we need to scroll the panel?\r
- if(av.getStartSeq()>index || av.getEndSeq()<index)\r
- alignPanel.setScrollValues( av.getStartRes(), index);\r
- }\r
-\r
- // this class allows scrolling off the bottom of the visible alignment\r
- class ScrollThread\r
- extends Thread\r
- {\r
- boolean running = false;\r
- boolean up = true;\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
- 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
- if(!up)\r
- seq = av.getEndSeq();\r
-\r
- if (seq < lastid)\r
- selectSeqs(lastid - 1, seq);\r
- else if (seq > lastid)\r
- selectSeqs(lastid + 1, seq);\r
-\r
- lastid = seq;\r
- }\r
- else\r
- running = false;\r
-\r
- alignPanel.repaint();\r
- try\r
- {\r
- Thread.sleep(100);\r
- }\r
- catch (Exception ex)\r
- {}\r
- }\r
- }\r
-}\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * 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.
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.util.Vector;
+
+import jalview.datamodel.*;
+import jalview.util.UrlLink;
+
+public class IdPanel extends Panel implements MouseListener,
+ MouseMotionListener
+{
+
+ protected IdCanvas idCanvas;
+
+ protected AlignViewport av;
+
+ protected AlignmentPanel alignPanel;
+
+ ScrollThread scrollThread = null;
+
+ int offy;
+
+ int width;
+
+ int lastid = -1;
+
+ boolean mouseDragging = false;
+
+ java.util.Vector links = new java.util.Vector();
+
+ public IdPanel(AlignViewport av, AlignmentPanel parent)
+ {
+ this.av = av;
+ alignPanel = parent;
+ idCanvas = new IdCanvas(av);
+ setLayout(new BorderLayout());
+ add(idCanvas, BorderLayout.CENTER);
+ idCanvas.addMouseListener(this);
+ idCanvas.addMouseMotionListener(this);
+
+ String label, url;
+ // TODO: add in group link parameter
+ if (av.applet != null)
+ {
+ for (int i = 1; i < 10; i++)
+ {
+ label = av.applet.getParameter("linkLabel_" + i);
+ url = av.applet.getParameter("linkURL_" + i);
+
+ if (label != null && url != null)
+ {
+ links.addElement(label + "|" + url);
+ }
+
+ }
+ }
+ if (links.size() < 1)
+ {
+ links = new java.util.Vector();
+ links.addElement("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+ }
+ }
+
+ Tooltip tooltip;
+
+ public void mouseMoved(MouseEvent e)
+ {
+ int seq = alignPanel.seqPanel.findSeq(e);
+
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+
+ // look for non-pos features
+ StringBuffer tooltiptext = new StringBuffer();
+ if (sequence != null)
+ {
+ if (sequence.getDescription() != null)
+ {
+ tooltiptext.append(sequence.getDescription());
+ tooltiptext.append("\n");
+ }
+
+ SequenceFeature sf[] = sequence.getSequenceFeatures();
+ for (int sl = 0; sf != null && sl < sf.length; sl++)
+ {
+ if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
+ {
+ boolean nl = false;
+ if (sf[sl].getFeatureGroup() != null)
+ {
+ tooltiptext.append(sf[sl].getFeatureGroup());
+ nl = true;
+ }
+ ;
+ if (sf[sl].getType() != null)
+ {
+ tooltiptext.append(" ");
+ tooltiptext.append(sf[sl].getType());
+ nl = true;
+ }
+ ;
+ if (sf[sl].getDescription() != null)
+ {
+ tooltiptext.append(" ");
+ tooltiptext.append(sf[sl].getDescription());
+ nl = true;
+ }
+ ;
+ if (sf[sl].getScore() != Float.NaN && sf[sl].getScore() != 0f)
+ {
+ tooltiptext.append(" Score = ");
+ tooltiptext.append(sf[sl].getScore());
+ nl = true;
+ }
+ ;
+ if (sf[sl].getStatus() != null && sf[sl].getStatus().length() > 0)
+ {
+ tooltiptext.append(" (");
+ tooltiptext.append(sf[sl].getStatus());
+ tooltiptext.append(")");
+ nl = true;
+ }
+ ;
+ if (nl)
+ {
+ tooltiptext.append("\n");
+ }
+ }
+ }
+ }
+ if (tooltiptext.length() == 0)
+ {
+ // nothing to display - so clear tooltip if one is visible
+ if (tooltip != null)
+ {
+ tooltip.setVisible(false);
+ }
+ tooltip = null;
+ tooltiptext = null;
+ return;
+ }
+ if (tooltip == null)
+ {
+ tooltip = new Tooltip(sequence.getDisplayId(true) + "\n"
+ + tooltiptext.toString(), idCanvas);
+ }
+ else
+ {
+ tooltip.setTip(sequence.getDisplayId(true) + "\n"
+ + tooltiptext.toString());
+ }
+ tooltiptext = null;
+ }
+
+ public void mouseDragged(MouseEvent e)
+ {
+ mouseDragging = true;
+
+ int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
+
+ if (seq < lastid)
+ {
+ selectSeqs(lastid - 1, seq);
+ }
+ else if (seq > lastid)
+ {
+ selectSeqs(lastid + 1, seq);
+ }
+
+ lastid = seq;
+ alignPanel.paintAlignment(false);
+ }
+
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() < 2)
+ {
+ return;
+ }
+
+ // DEFAULT LINK IS FIRST IN THE LINK LIST
+ int seq = alignPanel.seqPanel.findSeq(e);
+ SequenceI sq = av.getAlignment().getSequenceAt(seq);
+ if (sq==null)
+ {
+ return;
+ }
+ String id = sq.getName();
+
+ String target = null;
+ String url = null;
+ int i = 0;
+ while (url == null && i < links.size())
+ {
+ // DEFAULT LINK IS FIRST IN THE LINK LIST
+ // BUT IF ITS A REGEX AND DOES NOT MATCH THE NEXT ONE WILL BE TRIED
+ url = links.elementAt(i++).toString();
+ jalview.util.UrlLink urlLink = null;
+ try
+ {
+ urlLink = new UrlLink(url);
+ target = urlLink.getTarget();
+ } catch (Exception foo)
+ {
+ System.err.println("Exception for URLLink '" + url + "'");
+ foo.printStackTrace();
+ url = null;
+ continue;
+ }
+ ;
+ if (!urlLink.isValid())
+ {
+ System.err.println(urlLink.getInvalidMessage());
+ url = null;
+ continue;
+ }
+
+ String urls[] = urlLink.makeUrls(id, true);
+ if (urls == null || urls[0] == null || urls[0].length() < 1)
+ {
+ url = null;
+ continue;
+ }
+ // just take first URL made from regex
+ url = urls[1];
+ }
+ try
+ {
+
+ alignPanel.alignFrame.showURL(url, target);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ public void mouseEntered(MouseEvent e)
+ {
+ if (scrollThread != null)
+ {
+ scrollThread.running = false;
+ }
+ }
+
+ public void mouseExited(MouseEvent e)
+ {
+ if (av.getWrapAlignment())
+ {
+ return;
+ }
+
+ if (mouseDragging && e.getY() < 0 && av.getStartSeq() > 0)
+ {
+ scrollThread = new ScrollThread(true);
+ }
+
+ if (mouseDragging && e.getY() >= getSize().height
+ && av.alignment.getHeight() > av.getEndSeq())
+ {
+ scrollThread = new ScrollThread(false);
+ }
+ }
+
+ public void mousePressed(MouseEvent e)
+ {
+ if (e.getClickCount() > 1)
+ {
+ return;
+ }
+
+ int y = e.getY();
+ if (av.getWrapAlignment())
+ {
+ y -= 2 * av.charHeight;
+ }
+
+ int seq = alignPanel.seqPanel.findSeq(e);
+
+ if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ {
+ Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
+
+ // build a new links menu based on the current links + any non-positional
+ // features
+ Vector nlinks = new Vector();
+ for (int l = 0, lSize = links.size(); l < lSize; l++)
+ {
+ nlinks.addElement(links.elementAt(l));
+ }
+ SequenceFeature sf[] = sq==null ? null:sq.getSequenceFeatures();
+ for (int sl = 0; sf != null && sl < sf.length; sl++)
+ {
+ if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
+ {
+ if (sf[sl].links != null && sf[sl].links.size() > 0)
+ {
+ for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
+ {
+ nlinks.addElement(sf[sl].links.elementAt(l));
+ }
+ }
+ }
+ }
+
+ APopupMenu popup = new APopupMenu(alignPanel, sq, nlinks);
+ this.add(popup);
+ popup.show(this, e.getX(), e.getY());
+ return;
+ }
+
+ if ((av.getSelectionGroup() == null)
+ || ((!e.isControlDown() && !e.isShiftDown()) && av
+ .getSelectionGroup() != null))
+ {
+ av.setSelectionGroup(new SequenceGroup());
+ av.getSelectionGroup().setStartRes(0);
+ av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
+ }
+
+ if (e.isShiftDown() && lastid != -1)
+ {
+ selectSeqs(lastid, seq);
+ }
+ else
+ {
+ selectSeq(seq);
+ }
+
+ alignPanel.paintAlignment(false);
+ }
+
+ void selectSeq(int seq)
+ {
+ lastid = seq;
+ SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
+ av.getSelectionGroup().addOrRemove(pickedSeq, false);
+ }
+
+ void selectSeqs(int start, int end)
+ {
+
+ lastid = start;
+
+ if (end >= av.getAlignment().getHeight())
+ {
+ end = av.getAlignment().getHeight() - 1;
+ }
+
+ if (end < start)
+ {
+ int tmp = start;
+ start = end;
+ end = tmp;
+ lastid = end;
+ }
+ if (av.getSelectionGroup() == null)
+ {
+ av.setSelectionGroup(new SequenceGroup());
+ }
+ for (int i = start; i <= end; i++)
+ {
+ av.getSelectionGroup().addSequence(
+ av.getAlignment().getSequenceAt(i), false);
+ }
+
+ }
+
+ public void mouseReleased(MouseEvent e)
+ {
+ if (scrollThread != null)
+ {
+ scrollThread.running = false;
+ }
+
+ if (av.getSelectionGroup() != null)
+ {
+ av.getSelectionGroup().recalcConservation();
+ }
+
+ mouseDragging = false;
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ // always send selection message when mouse is released
+ av.sendSelection();
+ }
+
+ public void highlightSearchResults(java.util.Vector found)
+ {
+ idCanvas.setHighlighted(found);
+
+ if (found == null)
+ {
+ return;
+ }
+
+ int index = av.alignment.findIndex((SequenceI) found.elementAt(0));
+
+ // do we need to scroll the panel?
+ if (av.getStartSeq() > index || av.getEndSeq() < index)
+ {
+ alignPanel.setScrollValues(av.getStartRes(), index);
+ }
+ }
+
+ // this class allows scrolling off the bottom of the visible alignment
+ class ScrollThread extends Thread
+ {
+ boolean running = false;
+
+ boolean up = true;
+
+ public ScrollThread(boolean up)
+ {
+ this.up = up;
+ start();
+ }
+
+ public void stopScrolling()
+ {
+ running = false;
+ }
+
+ public void run()
+ {
+ running = true;
+ while (running)
+ {
+ if (alignPanel.scrollUp(up))
+ {
+ // scroll was ok, so add new sequence to selection
+ int seq = av.getStartSeq();
+ if (!up)
+ {
+ seq = av.getEndSeq();
+ }
+
+ if (seq < lastid)
+ {
+ selectSeqs(lastid - 1, seq);
+ }
+ else if (seq > lastid && seq < av.alignment.getHeight())
+ {
+ selectSeqs(lastid + 1, seq);
+ }
+
+ lastid = seq;
+ }
+ else
+ {
+ running = false;
+ }
+
+ alignPanel.paintAlignment(true);
+ try
+ {
+ Thread.sleep(100);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff