From 5d01e85b903f9ce67b2b4a32e9e7a02f57d9f2e9 Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 19 Aug 2008 09:37:52 +0000 Subject: [PATCH] regex links for launching URL from single click on sequence ID --- src/jalview/appletgui/IdPanel.java | 734 +++++++++++++++++++----------------- src/jalview/gui/IdPanel.java | 47 ++- 2 files changed, 415 insertions(+), 366 deletions(-) diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java index c510803..44a03ec 100755 --- a/src/jalview/appletgui/IdPanel.java +++ b/src/jalview/appletgui/IdPanel.java @@ -1,354 +1,380 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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; - -import java.awt.*; -import java.awt.event.*; - -import jalview.datamodel.*; - -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; - 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); - - 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()); - } - } - - 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); - 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 - { - - 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) - { - APopupMenu popup = new APopupMenu(alignPanel, - (Sequence) av.getAlignment(). - getSequenceAt(seq), links); - 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; - } - - 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()); - } - - 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) - {} - } - } - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 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; + +import java.awt.*; +import java.awt.event.*; + +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; + 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); + + 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()); + } + } + + 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); + String id = av.getAlignment().getSequenceAt(seq).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) + { + APopupMenu popup = new APopupMenu(alignPanel, + (Sequence) av.getAlignment(). + getSequenceAt(seq), links); + 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; + } + + 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()); + } + + 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) + {} + } + } + } + +} diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index d4e7c77..4741974 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -23,6 +23,7 @@ import java.awt.event.*; import javax.swing.*; import jalview.datamodel.*; +import jalview.util.UrlLink; /** * DOCUMENT ME! @@ -184,21 +185,42 @@ public class IdPanel } int seq = alignPanel.seqPanel.findSeq(e); - - //DEFAULT LINK IS FIRST IN THE LINK LIST - + String url = null; + int i = 0; String id = av.getAlignment().getSequenceAt(seq).getName(); - if (id.indexOf("|") > -1) + while (url == null && i < links.size()) { - id = id.substring(id.lastIndexOf("|") + 1); - } - - 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); + // 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); + } catch (Exception foo) + { + jalview.bin.Cache.log.error("Exception for URLLink '" + url + "'", + foo); + url = null; + continue; + } + ; + if (!urlLink.isValid()) + { + jalview.bin.Cache.log.error(urlLink.getInvalidMessage()); + url = null; + continue; + } + String urls[] = urlLink.makeUrls(id, true); + if (urls == null || urls[0]==null || urls[0].length()<4) + { + url = null; + continue; + } + // just take first URL made from regex + url = urls[1]; + } try { jalview.util.BrowserLauncher.openURL(url); @@ -213,6 +235,7 @@ public class IdPanel JOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } + } /** -- 1.7.10.2