-/*\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
-\r
-package jalview.appletgui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class IdPanel\r
- extends Panel implements MouseListener, MouseMotionListener\r
-{\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
- java.util.Vector links = new java.util.Vector();\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
- String label, url;\r
- if(parent.alignFrame.applet!=null)\r
- {\r
- for (int i = 1; i < 10; i++)\r
- {\r
- label = parent.alignFrame.applet.getParameter("linkLabel_" + i);\r
- url = parent.alignFrame.applet.getParameter("linkURL_" + i);\r
-\r
- if (label != null && url != null)\r
- links.addElement(label + "|" + url);\r
-\r
- }\r
- }\r
- if (links.size() < 1)\r
- {\r
- links = new java.util.Vector();\r
- links.addElement("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");\r
- }\r
- }\r
-\r
- Tooltip tooltip;\r
- public void mouseMoved(MouseEvent e)\r
- {\r
- int seq = alignPanel.seqPanel.findSeq(e);\r
-\r
- SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
-\r
- if(sequence.getDescription()==null)\r
- {\r
- if(tooltip!=null)\r
- tooltip.setVisible(false);\r
- tooltip = null;\r
- return;\r
- }\r
-\r
- if (tooltip == null)\r
- tooltip = new Tooltip(\r
- sequence.getDisplayId(true)\r
- + "\n" + sequence.getDescription(), idCanvas);\r
- else\r
- tooltip.setTip(sequence.getDisplayId(true)\r
- + "\n" + sequence.getDescription());\r
-\r
- tooltip.repaint();\r
-\r
- }\r
-\r
- public void mouseDragged(MouseEvent e)\r
- {\r
- mouseDragging = true;\r
-\r
- int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));\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
- alignPanel.repaint();\r
- }\r
-\r
- public void mouseClicked(MouseEvent e)\r
- {\r
- if (e.getClickCount() < 2)\r
- return;\r
-\r
-\r
- //DEFAULT LINK IS FIRST IN THE LINK LIST\r
- int seq = alignPanel.seqPanel.findSeq(e);\r
- String id = av.getAlignment().getSequenceAt(seq).getName();\r
- if (id.indexOf("|") > -1)\r
- id = id.substring(id.lastIndexOf("|") + 1);\r
-\r
- String target = links.elementAt(0).toString();\r
- target = target.substring(0, target.indexOf("|"));\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
-\r
- alignPanel.alignFrame.showURL(url, target);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- public void mouseEntered(MouseEvent e)\r
- {\r
- if (scrollThread != null)\r
- {\r
- scrollThread.running = false;\r
- }\r
- }\r
-\r
- public void mouseExited(MouseEvent e)\r
- {\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() >= getSize().height &&\r
- av.alignment.getHeight() > av.getEndSeq())\r
- {\r
- scrollThread = new ScrollThread(false);\r
- }\r
- }\r
-\r
- public void mousePressed(MouseEvent e)\r
- {\r
- if (e.getClickCount() >1 )\r
- {\r
- return;\r
- }\r
-\r
- int y = e.getY();\r
- if (av.getWrapAlignment())\r
- {\r
- y -= 2 * av.charHeight;\r
- }\r
-\r
- int seq = alignPanel.seqPanel.findSeq(e);\r
-\r
- if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) ==\r
- InputEvent.BUTTON3_MASK)\r
- {\r
- APopupMenu popup = new APopupMenu(alignPanel, (Sequence) av.getAlignment().getSequenceAt(seq), links);\r
- this.add(popup);\r
- popup.show(this, e.getX(), e.getY());\r
- return;\r
- }\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
- 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
- void selectSeq(int seq)\r
- {\r
- lastid = seq;\r
- SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);\r
- av.getSelectionGroup().addOrRemove(pickedSeq, false);\r
- }\r
-\r
- void selectSeqs(int start, int end)\r
- {\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
- {\r
- av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), false);\r
- }\r
-\r
- }\r
-\r
- public void mouseReleased(MouseEvent e)\r
- {\r
- if (scrollThread != null)\r
- {\r
- scrollThread.running = false;\r
- }\r
-\r
- if(av.getSelectionGroup()!=null)\r
- av.getSelectionGroup().recalcConservation();\r
-\r
- mouseDragging = false;\r
- PaintRefresher.Refresh(this, av.alignment);\r
- }\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.elementAt(0));\r
-\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
- // 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
- {\r
- seq = av.getEndSeq();\r
- }\r
-\r
- if (seq < lastid)\r
- {\r
- selectSeqs(lastid - 1, seq);\r
- }\r
- else if (seq > lastid && seq<av.alignment.getHeight())\r
- {\r
- selectSeqs(lastid + 1, seq);\r
- }\r
-\r
-\r
- lastid = seq;\r
- }\r
- else\r
- {\r
- running = false;\r
- }\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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.urls.api.UrlProviderFactoryI;
+import jalview.urls.api.UrlProviderI;
+import jalview.urls.applet.AppletUrlProviderFactory;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.BorderLayout;
+import java.awt.Panel;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+
+public class IdPanel extends Panel implements MouseListener,
+ MouseMotionListener
+{
+
+ protected IdCanvas idCanvas;
+
+ protected AlignmentViewport av;
+
+ protected AlignmentPanel alignPanel;
+
+ ScrollThread scrollThread = null;
+
+ int lastid = -1;
+
+ boolean mouseDragging = false;
+
+ UrlProviderI urlProvider = null;
+
+ public IdPanel(AlignViewport viewport, AlignmentPanel parent)
+ {
+ this.av = viewport;
+ alignPanel = parent;
+ idCanvas = new IdCanvas(viewport);
+ setLayout(new BorderLayout());
+ add(idCanvas, BorderLayout.CENTER);
+ idCanvas.addMouseListener(this);
+ idCanvas.addMouseMotionListener(this);
+
+ String label, url;
+ // TODO: add in group link parameter
+
+ // make a list of label,url pairs
+ HashMap<String, String> urlList = new HashMap<String, String>();
+ if (viewport.applet != null)
+ {
+ for (int i = 1; i < 10; i++)
+ {
+ label = viewport.applet.getParameter("linkLabel_" + i);
+ url = viewport.applet.getParameter("linkURL_" + i);
+
+ // only add non-null parameters
+ if (label != null)
+ {
+ urlList.put(label, url);
+ }
+ }
+
+ if (!urlList.isEmpty())
+ {
+ // set default as first entry in list
+ String defaultUrl = viewport.applet.getParameter("linkLabel_1");
+ UrlProviderFactoryI factory = new AppletUrlProviderFactory(
+ defaultUrl, urlList);
+ urlProvider = factory.createUrlProvider();
+ }
+ }
+ }
+
+ Tooltip tooltip;
+
+ @Override
+ public void mouseMoved(MouseEvent e)
+ {
+ int seq = alignPanel.seqPanel.findSeq(e);
+
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+
+ StringBuffer tooltiptext = new StringBuffer();
+ if (sequence == null)
+ {
+ return;
+ }
+ if (sequence.getDescription() != null)
+ {
+ tooltiptext.append(sequence.getDescription());
+ tooltiptext.append("\n");
+ }
+
+ for (SequenceFeature sf : sequence.getFeatures()
+ .getNonPositionalFeatures())
+ {
+ boolean nl = false;
+ if (sf.getFeatureGroup() != null)
+ {
+ tooltiptext.append(sf.getFeatureGroup());
+ nl = true;
+ }
+ if (sf.getType() != null)
+ {
+ tooltiptext.append(" ");
+ tooltiptext.append(sf.getType());
+ nl = true;
+ }
+ if (sf.getDescription() != null)
+ {
+ tooltiptext.append(" ");
+ tooltiptext.append(sf.getDescription());
+ nl = true;
+ }
+ if (!Float.isNaN(sf.getScore()) && sf.getScore() != 0f)
+ {
+ tooltiptext.append(" Score = ");
+ tooltiptext.append(sf.getScore());
+ nl = true;
+ }
+ if (sf.getStatus() != null && sf.getStatus().length() > 0)
+ {
+ tooltiptext.append(" (");
+ tooltiptext.append(sf.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;
+ }
+
+ @Override
+ 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);
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() < 2)
+ {
+ return;
+ }
+
+ // get the sequence details
+ int seq = alignPanel.seqPanel.findSeq(e);
+ SequenceI sq = av.getAlignment().getSequenceAt(seq);
+ if (sq == null)
+ {
+ return;
+ }
+ String id = sq.getName();
+
+ // get the default url with the sequence details filled in
+ if (urlProvider == null)
+ {
+ return;
+ }
+ String url = urlProvider.getPrimaryUrl(id);
+ String target = urlProvider.getPrimaryTarget(id);
+ try
+ {
+ alignPanel.alignFrame.showURL(url, target);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ if (scrollThread != null)
+ {
+ scrollThread.running = false;
+ }
+ }
+
+ @Override
+ public void mouseExited(MouseEvent e)
+ {
+ if (av.getWrapAlignment())
+ {
+ return;
+ }
+
+ if (mouseDragging && e.getY() < 0 && av.getRanges().getStartSeq() > 0)
+ {
+ scrollThread = new ScrollThread(true);
+ }
+
+ if (mouseDragging && e.getY() >= getSize().height
+ && av.getAlignment().getHeight() > av.getRanges().getEndSeq())
+ {
+ scrollThread = new ScrollThread(false);
+ }
+ }
+
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ if (e.getClickCount() > 1)
+ {
+ return;
+ }
+
+ int y = e.getY();
+ if (av.getWrapAlignment())
+ {
+ y -= 2 * av.getCharHeight();
+ }
+
+ int seq = alignPanel.seqPanel.findSeq(e);
+
+ if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ {
+ SequenceI sq = av.getAlignment().getSequenceAt(seq);
+
+ /*
+ * build a new links menu based on the current links
+ * and any non-positional features
+ */
+ List<String> nlinks;
+ if (urlProvider != null)
+ {
+ nlinks = urlProvider.getLinksForMenu();
+ }
+ else
+ {
+ nlinks = new ArrayList<String>();
+ }
+
+ for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
+ {
+ if (sf.links != null)
+ {
+ for (String link : sf.links)
+ {
+ nlinks.add(link);
+ }
+ }
+ }
+
+ APopupMenu popup = new APopupMenu(alignPanel, sq, nlinks);
+ this.add(popup);
+ popup.show(this, e.getX(), e.getY());
+ return;
+ }
+
+ if ((av.getSelectionGroup() == null)
+ || ((!jalview.util.Platform.isControlDown(e) && !e
+ .isShiftDown()) && av.getSelectionGroup() != null))
+ {
+ av.setSelectionGroup(new SequenceGroup());
+ av.getSelectionGroup().setStartRes(0);
+ av.getSelectionGroup().setEndRes(av.getAlignment().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, true);
+ }
+
+ 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), i == end);
+ }
+
+ }
+
+ @Override
+ 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(List<SequenceI> list)
+ {
+ idCanvas.setHighlighted(list);
+
+ if (list == null)
+ {
+ return;
+ }
+
+ int index = av.getAlignment().findIndex(list.get(0));
+
+ // do we need to scroll the panel?
+ if (av.getRanges().getStartSeq() > index
+ || av.getRanges().getEndSeq() < index)
+ {
+ av.getRanges().setStartSeq(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 isUp)
+ {
+ this.up = isUp;
+ start();
+ }
+
+ public void stopScrolling()
+ {
+ running = false;
+ }
+
+ @Override
+ public void run()
+ {
+ running = true;
+ while (running)
+ {
+ if (av.getRanges().scrollUp(up))
+ {
+ // scroll was ok, so add new sequence to selection
+ int seq = av.getRanges().getStartSeq();
+ if (!up)
+ {
+ seq = av.getRanges().getEndSeq();
+ }
+
+ if (seq < lastid)
+ {
+ selectSeqs(lastid - 1, seq);
+ }
+ else if (seq > lastid && seq < av.getAlignment().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