From 8dd1cd955b1c6f1a89afc2068ab1cdfca3824934 Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 30 Jun 2008 10:49:49 +0000 Subject: [PATCH] javadoc and constraint to ensure annotation labels are not wider than alignment frame --- src/jalview/gui/AlignmentPanel.java | 9 +- src/jalview/gui/IdPanel.java | 896 +++++++++++++++++------------------ 2 files changed, 453 insertions(+), 452 deletions(-) diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 326ac07..95b4220 100755 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -154,9 +154,9 @@ public class AlignmentPanel } /** - * DOCUMENT ME! + * Calculate the width of the alignment labels based on the displayed names and any bounds on label width set in preferences. * - * @return DOCUMENT ME! + * @return Dimension giving the maximum width of the alignment label panel that should be used. */ public Dimension calculateIdWidth() { @@ -166,7 +166,8 @@ public class AlignmentPanel new Font(av.font.getName(), Font.ITALIC, av.font.getSize())); AlignmentI al = av.getAlignment(); - + int afwidth = (alignFrame!=null ? alignFrame.getWidth() : 300); + int maxwidth = Math.max(20,Math.min(afwidth-200,(int) 2*afwidth/3)); int i = 0; int idWidth = 0; String id; @@ -205,7 +206,7 @@ public class AlignmentPanel } } - return new Dimension(idWidth, 12); + return new Dimension(Math.min(maxwidth, idWidth), 12); } /** diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index b9366ae..d4e7c77 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -1,448 +1,448 @@ -/* - * 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.gui; - -import java.awt.*; -import java.awt.event.*; -import javax.swing.*; - -import jalview.datamodel.*; - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class IdPanel - extends JPanel implements MouseListener, - MouseMotionListener, MouseWheelListener -{ - protected IdCanvas idCanvas; - protected AlignViewport av; - protected AlignmentPanel alignPanel; - ScrollThread scrollThread = null; - int offy; - int width; - int lastid = -1; - boolean mouseDragging = false; - - /** - * Creates a new IdPanel object. - * - * @param av DOCUMENT ME! - * @param parent DOCUMENT ME! - */ - public IdPanel(AlignViewport av, AlignmentPanel parent) - { - this.av = av; - alignPanel = parent; - idCanvas = new IdCanvas(av); - setLayout(new BorderLayout()); - add(idCanvas, BorderLayout.CENTER); - addMouseListener(this); - addMouseMotionListener(this); - addMouseWheelListener(this); - ToolTipManager.sharedInstance().registerComponent(this); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mouseMoved(MouseEvent e) - { - int seq = Math.max(0, alignPanel.seqPanel.findSeq(e)); - String tmp; - if (seq > -1 && seq < av.alignment.getHeight()) - { - SequenceI sequence = av.alignment.getSequenceAt(seq); - StringBuffer tip = new StringBuffer(); - tip.append(""); - - int maxWidth = 0; - if (sequence.getDescription() != null) - { - tmp = sequence.getDescription(); - tip.append("
"+tmp); - maxWidth = Math.max(maxWidth, tmp.length()); - } - - DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef(); - if (dbrefs != null) - { - for (int i = 0; i < dbrefs.length; i++) - { - tip.append("
"); - tmp = dbrefs[i].getSource() + " " + dbrefs[i].getAccessionId(); - tip.append(tmp); - maxWidth = Math.max(maxWidth, tmp.length()); - } - } - - - //ADD NON POSITIONAL SEQUENCE INFO - SequenceFeature[] features = sequence.getDatasetSequence(). - getSequenceFeatures(); - if (features != null) - { - for (int i = 0; i < features.length; i++) - { - if (features[i].begin == 0 && features[i].end == 0) - { - tmp = features[i].featureGroup - + " " + features[i].getType() + " " + - features[i].description; - tip.append("
" + tmp); - maxWidth = Math.max(maxWidth, tmp.length()); - } - } - } - - if(maxWidth > 60) - { - tip.insert(0, "
"); - tip.append("
"); - } - - tip.append(""); - - setToolTipText(""+sequence.getDisplayId(true)+tip.toString()); - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - 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(true); - } - - public void mouseWheelMoved(MouseWheelEvent e) - { - e.consume(); - if (e.getWheelRotation() > 0) - { - alignPanel.scrollUp(false); - } - else - { - alignPanel.scrollUp(true); - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mouseClicked(MouseEvent e) - { - if (e.getClickCount() < 2) - { - return; - } - - java.util.Vector links = Preferences.sequenceURLLinks; - if (links == null || links.size() < 1) - { - return; - } - - int seq = alignPanel.seqPanel.findSeq(e); - - //DEFAULT LINK IS FIRST IN THE LINK LIST - - String id = av.getAlignment().getSequenceAt(seq).getName(); - if (id.indexOf("|") > -1) - { - 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); - - try - { - jalview.util.BrowserLauncher.openURL(url); - } - catch (Exception ex) - { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Unixers: Couldn't find default web browser." - + - "\nAdd the full path to your browser in Preferences.", - "Web browser not found", - JOptionPane.WARNING_MESSAGE); - ex.printStackTrace(); - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mouseEntered(MouseEvent e) - { - if (scrollThread != null) - { - scrollThread.running = false; - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - 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() >= getHeight()) && - (av.alignment.getHeight() > av.getEndSeq())) - { - scrollThread = new ScrollThread(false); - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mousePressed(MouseEvent e) - { - if (e.getClickCount() == 2) - { - return; - } - - int seq = alignPanel.seqPanel.findSeq(e); - - if (javax.swing.SwingUtilities.isRightMouseButton(e)) - { - jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel, - (Sequence) av.getAlignment().getSequenceAt(seq), - Preferences.sequenceURLLinks); - pop.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(true); - } - - /** - * DOCUMENT ME! - * - * @param seq DOCUMENT ME! - */ - void selectSeq(int seq) - { - lastid = seq; - - SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); - av.getSelectionGroup().addOrRemove(pickedSeq, true); - } - - /** - * DOCUMENT ME! - * - * @param start DOCUMENT ME! - * @param end DOCUMENT ME! - */ - void selectSeqs(int start, int end) - { - if (av.getSelectionGroup() == null) - { - return; - } - - if (end >= av.getAlignment().getHeight()) - { - end = av.getAlignment().getHeight() - 1; - } - - 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), - true); - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mouseReleased(MouseEvent e) - { - if (scrollThread != null) - { - scrollThread.running = false; - } - - mouseDragging = false; - PaintRefresher.Refresh(this, av.getSequenceSetId()); - } - - /** - * DOCUMENT ME! - * - * @param found DOCUMENT ME! - */ - public void highlightSearchResults(java.util.Vector found) - { - idCanvas.setHighlighted(found); - - if (found == null) - { - return; - } - - int index = av.alignment.findIndex( (SequenceI) found.get(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) - { - selectSeqs(lastid + 1, seq); - } - - lastid = seq; - } - else - { - running = false; - } - - alignPanel.paintAlignment(false); - - 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.gui; + +import java.awt.*; +import java.awt.event.*; +import javax.swing.*; + +import jalview.datamodel.*; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class IdPanel + extends JPanel implements MouseListener, + MouseMotionListener, MouseWheelListener +{ + protected IdCanvas idCanvas; + protected AlignViewport av; + protected AlignmentPanel alignPanel; + ScrollThread scrollThread = null; + int offy; + // int width; + int lastid = -1; + boolean mouseDragging = false; + + /** + * Creates a new IdPanel object. + * + * @param av DOCUMENT ME! + * @param parent DOCUMENT ME! + */ + public IdPanel(AlignViewport av, AlignmentPanel parent) + { + this.av = av; + alignPanel = parent; + idCanvas = new IdCanvas(av); + setLayout(new BorderLayout()); + add(idCanvas, BorderLayout.CENTER); + addMouseListener(this); + addMouseMotionListener(this); + addMouseWheelListener(this); + ToolTipManager.sharedInstance().registerComponent(this); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseMoved(MouseEvent e) + { + int seq = Math.max(0, alignPanel.seqPanel.findSeq(e)); + String tmp; + if (seq > -1 && seq < av.alignment.getHeight()) + { + SequenceI sequence = av.alignment.getSequenceAt(seq); + StringBuffer tip = new StringBuffer(); + tip.append(""); + + int maxWidth = 0; + if (sequence.getDescription() != null) + { + tmp = sequence.getDescription(); + tip.append("
"+tmp); + maxWidth = Math.max(maxWidth, tmp.length()); + } + + DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef(); + if (dbrefs != null) + { + for (int i = 0; i < dbrefs.length; i++) + { + tip.append("
"); + tmp = dbrefs[i].getSource() + " " + dbrefs[i].getAccessionId(); + tip.append(tmp); + maxWidth = Math.max(maxWidth, tmp.length()); + } + } + + + //ADD NON POSITIONAL SEQUENCE INFO + SequenceFeature[] features = sequence.getDatasetSequence(). + getSequenceFeatures(); + if (features != null) + { + for (int i = 0; i < features.length; i++) + { + if (features[i].begin == 0 && features[i].end == 0) + { + tmp = features[i].featureGroup + + " " + features[i].getType() + " " + + features[i].description; + tip.append("
" + tmp); + maxWidth = Math.max(maxWidth, tmp.length()); + } + } + } + + if(maxWidth > 60) + { + tip.insert(0, "
"); + tip.append("
"); + } + + tip.append(""); + + setToolTipText(""+sequence.getDisplayId(true)+tip.toString()); + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + 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(true); + } + + public void mouseWheelMoved(MouseWheelEvent e) + { + e.consume(); + if (e.getWheelRotation() > 0) + { + alignPanel.scrollUp(false); + } + else + { + alignPanel.scrollUp(true); + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseClicked(MouseEvent e) + { + if (e.getClickCount() < 2) + { + return; + } + + java.util.Vector links = Preferences.sequenceURLLinks; + if (links == null || links.size() < 1) + { + return; + } + + int seq = alignPanel.seqPanel.findSeq(e); + + //DEFAULT LINK IS FIRST IN THE LINK LIST + + String id = av.getAlignment().getSequenceAt(seq).getName(); + if (id.indexOf("|") > -1) + { + 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); + + try + { + jalview.util.BrowserLauncher.openURL(url); + } + catch (Exception ex) + { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "Unixers: Couldn't find default web browser." + + + "\nAdd the full path to your browser in Preferences.", + "Web browser not found", + JOptionPane.WARNING_MESSAGE); + ex.printStackTrace(); + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseEntered(MouseEvent e) + { + if (scrollThread != null) + { + scrollThread.running = false; + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + 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() >= getHeight()) && + (av.alignment.getHeight() > av.getEndSeq())) + { + scrollThread = new ScrollThread(false); + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mousePressed(MouseEvent e) + { + if (e.getClickCount() == 2) + { + return; + } + + int seq = alignPanel.seqPanel.findSeq(e); + + if (javax.swing.SwingUtilities.isRightMouseButton(e)) + { + jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel, + (Sequence) av.getAlignment().getSequenceAt(seq), + Preferences.sequenceURLLinks); + pop.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(true); + } + + /** + * DOCUMENT ME! + * + * @param seq DOCUMENT ME! + */ + void selectSeq(int seq) + { + lastid = seq; + + SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); + av.getSelectionGroup().addOrRemove(pickedSeq, true); + } + + /** + * DOCUMENT ME! + * + * @param start DOCUMENT ME! + * @param end DOCUMENT ME! + */ + void selectSeqs(int start, int end) + { + if (av.getSelectionGroup() == null) + { + return; + } + + if (end >= av.getAlignment().getHeight()) + { + end = av.getAlignment().getHeight() - 1; + } + + 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), + true); + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseReleased(MouseEvent e) + { + if (scrollThread != null) + { + scrollThread.running = false; + } + + mouseDragging = false; + PaintRefresher.Refresh(this, av.getSequenceSetId()); + } + + /** + * DOCUMENT ME! + * + * @param found DOCUMENT ME! + */ + public void highlightSearchResults(java.util.Vector found) + { + idCanvas.setHighlighted(found); + + if (found == null) + { + return; + } + + int index = av.alignment.findIndex( (SequenceI) found.get(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) + { + selectSeqs(lastid + 1, seq); + } + + lastid = seq; + } + else + { + running = false; + } + + alignPanel.paintAlignment(false); + + try + { + Thread.sleep(100); + } + catch (Exception ex) + { + } + } + } + } +} -- 1.7.10.2