X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=f66f445094e5c9726eb43c079b896a5a823b4f2d;hb=8240aa86ee94d4c372af7deb1452a8294ff8800b;hp=4998360a1eef268f4084dbc2d07947f00595ffc0;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java index 4998360..f66f445 100755 --- a/src/jalview/appletgui/IdPanel.java +++ b/src/jalview/appletgui/IdPanel.java @@ -1,21 +1,21 @@ /* -* 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 -*/ + * 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; @@ -24,47 +24,92 @@ import java.awt.event.*; import jalview.datamodel.*; -public class IdPanel extends Panel implements MouseListener, MouseMotionListener { +public class IdPanel + extends Panel implements MouseListener, MouseMotionListener +{ - protected IdCanvas idCanvas; - protected AlignViewport av; + protected IdCanvas idCanvas; + protected AlignViewport av; protected AlignmentPanel alignPanel; ScrollThread scrollThread = null; - int offy; - int width; + 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; + this.av = av; alignPanel = parent; idCanvas = new IdCanvas(av); setLayout(new BorderLayout()); add(idCanvas, BorderLayout.CENTER); idCanvas.addMouseListener(this); idCanvas.addMouseMotionListener(this); - } - public void mouseMoved(MouseEvent e) {} + String label, url; + 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); - public void mouseDragged(MouseEvent e) { - mouseDragging = true; + } + } + 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"); + } + } - int y = e.getY(); - if(av.getWrapAlignment()) - y-=2*av.charHeight; - int seq = av.getIndex(y); + Tooltip tooltip; + public void mouseMoved(MouseEvent e) + { + int seq = alignPanel.seqPanel.findSeq(e); + + SequenceI sequence = av.getAlignment().getSequenceAt(seq); - if(seq<0) + if(sequence.getDescription()==null) + { + if(tooltip!=null) + tooltip.setVisible(false); + tooltip = null; return; + } + + if (tooltip == null) + tooltip = new Tooltip( + sequence.getDisplayId(true) + + "\n" + sequence.getDescription(), idCanvas); + else + tooltip.setTip(sequence.getDisplayId(true) + + "\n" + sequence.getDescription()); + + tooltip.repaint(); + + } + + 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.repaint(); @@ -72,91 +117,104 @@ public class IdPanel extends Panel implements MouseListener, MouseMotionListener public void mouseClicked(MouseEvent e) { - if (e.getClickCount() == 2) + if (e.getClickCount() < 2) + return; + + + //DEFAULT LINK IS FIRST IN THE LINK LIST + int seq = alignPanel.seqPanel.findSeq(e); + String id = av.getAlignment().getSequenceAt(seq).getName(); + if (id.indexOf("|") > -1) + id = id.substring(id.lastIndexOf("|") + 1); + + String target = links.elementAt(0).toString(); + target = target.substring(0, target.indexOf("|")); + String url = links.elementAt(0).toString(); + url = url.substring(url.indexOf("|")+1); + + int index = url.indexOf("$SEQUENCE_ID$"); + url = url.substring(0, index)+ id + url.substring(index+13); + + try { - int y = e.getY(); - if(av.getWrapAlignment()) - y-=2*av.charHeight; - - int seq = av.getIndex(y); - String id = av.getAlignment().getSequenceAt(seq).getName(); - - try{ - jalview.bin.JalviewLite.showURL( - "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" + id + - "]+-vn+2"); - }catch(Exception ex){ex.printStackTrace();} - } + alignPanel.alignFrame.showURL(url, target); + } + catch (Exception ex) + { + ex.printStackTrace(); + } } + public void mouseEntered(MouseEvent e) { - if(scrollThread!=null) + if (scrollThread != null) + { scrollThread.running = false; + } } - public void mouseExited (MouseEvent e) + public void mouseExited(MouseEvent e) { - if(av.getWrapAlignment()) + if (av.getWrapAlignment()) + { return; + } - if(mouseDragging && e.getY()<0 && av.getStartSeq()>0) + if (mouseDragging && e.getY() < 0 && av.getStartSeq() > 0) { scrollThread = new ScrollThread(true); } - if(mouseDragging && e.getY()>=getSize().height && av.alignment.getHeight()>av.getEndSeq()) + if (mouseDragging && e.getY() >= getSize().height && + av.alignment.getHeight() > av.getEndSeq()) { scrollThread = new ScrollThread(false); } } - - public void mousePressed(MouseEvent e) { - if (e.getClickCount() == 2) + public void mousePressed(MouseEvent e) + { + if (e.getClickCount() >1 ) + { return; + } int y = e.getY(); - if(av.getWrapAlignment()) - y-=2*av.charHeight; + if (av.getWrapAlignment()) + { + y -= 2 * av.charHeight; + } - int seq = av.getIndex(y); - if (seq == -1) - return; + int seq = alignPanel.seqPanel.findSeq(e); - if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK) + if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) == + InputEvent.BUTTON3_MASK) { - APopupMenu popup = new APopupMenu(alignPanel, null); + APopupMenu popup = new APopupMenu(alignPanel, (Sequence) av.getAlignment().getSequenceAt(seq), links); this.add(popup); popup.show(this, e.getX(), e.getY()); return; } - if(!e.isControlDown() && !e.isShiftDown() && av.alignment.findGroup( av.alignment.getSequenceAt(seq))!=null) + if ((av.getSelectionGroup() == null) || + ((!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null)) { - - SequenceGroup selection = new SequenceGroup(); - SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(seq)); - selection.setStartRes(0); - selection.setEndRes(av.alignment.getWidth()-1); - for (int i =0; i< sg.getSize(); i++) - selection.addSequence(sg.getSequenceAt(i)); - - av.setSelectionGroup(selection); - return; - } - - if(av.getSelectionGroup()==null || ( !e.isControlDown() && av.getSelectionGroup()!=null)) av.setSelectionGroup(new SequenceGroup()); + av.getSelectionGroup().setStartRes(0); + av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1); + } - av.getSelectionGroup().setStartRes(0); - av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1); - if(e.isShiftDown() && lastid!=-1) + if (e.isShiftDown() && lastid != -1) + { selectSeqs(lastid, seq); + } else + { selectSeq(seq); + } alignPanel.repaint(); } @@ -165,47 +223,58 @@ public class IdPanel extends Panel implements MouseListener, MouseMotionListener { lastid = seq; SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); - av.getSelectionGroup().addOrRemove(pickedSeq); + av.getSelectionGroup().addOrRemove(pickedSeq, false); } - void selectSeqs(int start, int end) { + void selectSeqs(int start, int end) + { lastid = start; if (end < start) - { - int tmp = start; - start = end; - end = tmp; - lastid = end; - } - - for (int i = start; i <= end; i++) - av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i)); + { + int tmp = start; + start = end; + end = tmp; + lastid = end; + } - } + for (int i = start; i <= end; i++) + { + av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), false); + } + } public void mouseReleased(MouseEvent e) { - if(scrollThread!=null) + if (scrollThread != null) + { scrollThread.running = false; + } + + if(av.getSelectionGroup()!=null) + av.getSelectionGroup().recalcConservation(); mouseDragging = false; - PaintRefresher.Refresh(this); + PaintRefresher.Refresh(this, av.alignment); } - public void highlightSearchResults( java.util.Vector found ) + public void highlightSearchResults(java.util.Vector found) { - idCanvas.setHighlighted( found ); + idCanvas.setHighlighted(found); - if(found == null) + if (found == null) + { return; + } - int index = av.alignment.findIndex( (SequenceI)found.elementAt(0)); + int index = av.alignment.findIndex( (SequenceI) found.elementAt(0)); // do we need to scroll the panel? - if(av.getStartSeq()>index || av.getEndSeq() index || av.getEndSeq() < index) + { + alignPanel.setScrollValues(av.getStartRes(), index); + } } // this class allows scrolling off the bottom of the visible alignment @@ -230,22 +299,31 @@ public class IdPanel extends Panel implements MouseListener, MouseMotionListener running = true; while (running) { - if(alignPanel.scrollUp(up)) + if (alignPanel.scrollUp(up)) { // scroll was ok, so add new sequence to selection int seq = av.getStartSeq(); - if(!up) + if (!up) + { seq = av.getEndSeq(); + } if (seq < lastid) + { selectSeqs(lastid - 1, seq); - else if (seq > lastid) + } + else if (seq > lastid && seq