X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=3dd7b5b34ca4a44ca95cd0f222afba27d0e9a902;hb=20c23143772b747cdd829e992cdea4cb1df59bd7;hp=4236cf8666111e47e94d52752f77a892a294451f;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 4236cf8..3dd7b5b 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -1,46 +1,45 @@ /* -* 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) 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 + */ package jalview.gui; import java.awt.*; import java.awt.event.*; - -import jalview.datamodel.*; - import javax.swing.*; -public class IdPanel extends JPanel implements MouseListener, MouseMotionListener { +import jalview.datamodel.*; - protected IdCanvas idCanvas; - protected AlignViewport av; +public class IdPanel + extends JPanel implements MouseListener, + MouseMotionListener +{ + 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; public IdPanel(AlignViewport av, AlignmentPanel parent) { - this.av = av; + this.av = av; alignPanel = parent; idCanvas = new IdCanvas(av); setLayout(new BorderLayout()); @@ -49,24 +48,36 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene addMouseMotionListener(this); } - public void mouseMoved(MouseEvent e) {} - + public void mouseMoved(MouseEvent e) + { + } - public void mouseDragged(MouseEvent e) { + public void mouseDragged(MouseEvent e) + { mouseDragging = true; 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<0) + if (seq < 0) + { return; + } if (seq < lastid) + { selectSeqs(lastid - 1, seq); + } else if (seq > lastid) + { selectSeqs(lastid + 1, seq); + } lastid = seq; alignPanel.repaint(); @@ -76,95 +87,128 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene { if (e.getClickCount() == 2) { - 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.util.BrowserLauncher.openURL( - "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" + id + - "]+-vn+2"); - }catch(Exception ex){ - // TODO: JBPNote : state dependent error message for real browserLaunch problems rather than unix misconfiguration. - System.err.println( - ex.getMessage()+"\nUnixers: Try adding this jalview.browser property line \n" - +"in your jalview.properties file (/usr/local/bin/firefox is an exanmple browser path):\n" - +"jalview.browser=/usr/local/bin/firefox\n"); - //ex.printStackTrace(); - } - } + 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.util.BrowserLauncher.openURL( + "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:" + + id + "]+-vn+2"); + } + catch (Exception ex) + { + // TODO: JBPNote : state dependent error message for real browserLaunch problems rather than unix misconfiguration. + System.err.println(ex.getMessage() + + "\nUnixers: Try adding this jalview.browser property line \n" + + "in your jalview.properties file (/usr/local/bin/firefox is an exanmple browser path):\n" + + "jalview.browser=/usr/local/bin/firefox\n"); + + //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()>=getHeight() && av.alignment.getHeight()>av.getEndSeq()) + if (mouseDragging && (e.getY() >= getHeight()) && + (av.alignment.getHeight() > av.getEndSeq())) { scrollThread = new ScrollThread(false); } } - - public void mousePressed(MouseEvent e) { + public void mousePressed(MouseEvent e) + { if (e.getClickCount() == 2) + { 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; + } if (javax.swing.SwingUtilities.isRightMouseButton(e)) { jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel, - (Sequence)av.getAlignment().getSequenceAt(seq)); + (Sequence) av.getAlignment().getSequenceAt(seq)); pop.show(this, e.getX(), y); + return; } - if(!e.isControlDown() && !e.isShiftDown() && av.alignment.findGroup( av.alignment.getSequenceAt(seq))!=null) + if (!e.isControlDown() && !e.isShiftDown() && + (av.alignment.findGroup(av.alignment.getSequenceAt(seq)) != null)) { - SequenceGroup selection = new SequenceGroup(); - SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(seq)); + 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)); + selection.setEndRes(av.alignment.getWidth() - 1); + + for (int i = 0; i < sg.getSize(); i++) + { + selection.addSequence(sg.getSequenceAt(i), true); + } av.setSelectionGroup(selection); + return; } - if(av.getSelectionGroup()==null || ( !e.isControlDown() && av.getSelectionGroup()!=null)) + 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().setEndRes(av.alignment.getWidth() - 1); - if(e.isShiftDown() && lastid!=-1) + if (e.isShiftDown() && (lastid != -1)) + { selectSeqs(lastid, seq); + } else + { selectSeq(seq); + } alignPanel.repaint(); } @@ -172,48 +216,56 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene void selectSeq(int seq) { lastid = seq; + SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); - av.getSelectionGroup().addOrRemove(pickedSeq); + av.getSelectionGroup().addOrRemove(pickedSeq, true); } - 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)); - } + 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), true); + } + } public void mouseReleased(MouseEvent e) { - if(scrollThread!=null) + if (scrollThread != null) + { scrollThread.running = false; + } mouseDragging = false; - PaintRefresher.Refresh(this); + PaintRefresher.Refresh(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.get(0)); + int index = av.alignment.findIndex( (SequenceI) found.get(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 @@ -222,6 +274,7 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene { boolean running = false; boolean up = true; + public ScrollThread(boolean up) { this.up = up; @@ -236,34 +289,45 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene public void run() { 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) + { selectSeqs(lastid + 1, seq); + } lastid = seq; } else + { running = false; + } alignPanel.repaint(); + try { Thread.sleep(100); } catch (Exception ex) - {} + { + } } } -} - + } }