X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=5727e9cccf6a427c56da2d6d9d41a90e123dc0ae;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=1a83b0900a0645d0827378c262df7ccb0bd1e891;hpb=9fff97021c2c637e426f6971d54dcf3fd4191985;p=jalview.git
diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 1a83b09..5727e9c 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,195 +1,872 @@
-/*
- * 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.appletgui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-
-public class AnnotationLabels
- extends Panel implements ActionListener
-{
- boolean active = false;
- AlignmentPanel ap;
- boolean resizing = false;
- int oldY, mouseX;
- static String ADDNEW = "Add new row";
- static String HIDE = "Hide this row";
- static String DELETE = "Delete this row";
- static String SHOWALL = "Show all hidden rows";
- static String OUTPUT_TEXT = "Show Values In Textbox";
- int selectedRow = 0;
- int scrollOffset = 0;
-
- public AnnotationLabels(AlignmentPanel ap)
- {
- this.ap = ap;
- setLayout(null);
- addMouseListener(new MouseAdapter()
- {
- public void mousePressed(MouseEvent evt)
- {
- doMousePressed(evt);
- }
- });
- }
-
- public void setScrollOffset(int y)
- {
- scrollOffset = y;
- repaint();
- }
-
- public void actionPerformed(ActionEvent evt)
- {
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
- if (evt.getActionCommand().equals(HIDE))
- {
- aa[selectedRow].visible = false;
- }
- else if (evt.getActionCommand().equals(SHOWALL))
- {
- for (int i = 0; i < aa.length; i++)
- {
- aa[i].visible = true;
- }
- }
- else if (evt.getActionCommand().equals(OUTPUT_TEXT))
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame,
- ap.alignFrame.getTitle() + " - " +
- aa[selectedRow].label, 500, 100);
- cap.setText(aa[selectedRow].toString());
- }
-
- ap.annotationPanel.adjustPanelHeight();
- setSize(getSize().width, ap.annotationPanel.getSize().height);
- ap.validate();
- ap.repaint();
- }
-
- public void doMousePressed(MouseEvent evt)
- {
- int y = evt.getY() - scrollOffset;
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
- int height = 0;
- for (int i = 0; i < aa.length; i++)
- {
- if (!aa[i].visible)
- {
- continue;
- }
-
- height += aa[i].height;
- if (y < height)
- {
- selectedRow = i;
- break;
- }
- }
-
- PopupMenu pop = new PopupMenu("Annotations");
- MenuItem item = new MenuItem(HIDE);
- item.addActionListener(this);
- pop.add(item);
- item = new MenuItem(SHOWALL);
- item.addActionListener(this);
- pop.add(item);
- this.add(pop);
- item = new MenuItem(OUTPUT_TEXT);
- item.addActionListener(this);
- pop.add(item);
-
- if (aa[selectedRow].label.equals("Consensus"))
- {
- pop.addSeparator();
- final CheckboxMenuItem cbmi = new CheckboxMenuItem(
- "Ignore gaps in calculation",
- ap.av.getIgnoreGapsConsensus());
-
- cbmi.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent e)
- {
- ap.av.setIgnoreGapsConsensus(cbmi.getState());
- ap.repaint();
- }
- });
- pop.add(cbmi);
- }
-
- pop.show(this, evt.getX(), evt.getY());
-
- }
-
- public void paint(Graphics g)
- {
- drawComponent(g);
- }
-
- public void drawComponent(Graphics g)
- {
- FontMetrics fm = g.getFontMetrics(g.getFont());
- g.setColor(Color.white);
- g.fillRect(0, 0, getSize().width, getSize().height);
-
- g.translate(0, scrollOffset);
- g.setColor(Color.black);
-
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
- int y = g.getFont().getSize();
- int x = 0;
-
- if (aa != null)
- {
- for (int i = 0; i < aa.length; i++)
- {
- if (!aa[i].visible)
- {
- continue;
- }
-
- x = getSize().width - fm.stringWidth(aa[i].label) - 3;
-
- if (aa[i].isGraph)
- {
- y += (aa[i].height / 3);
- }
-
- g.drawString(aa[i].label, x, y);
-
- if (aa[i].isGraph)
- {
- y += (2 * aa[i].height / 3);
- }
- else
- {
- y += aa[i].height;
- }
- }
- }
- }
-
-}
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+import jalview.util.ParseHtmlBodyAndLinks;
+
+import java.awt.Checkbox;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.PopupMenu;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.InputEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Vector;
+
+public class AnnotationLabels extends Panel implements ActionListener,
+ MouseListener, MouseMotionListener
+{
+ Image image;
+
+ boolean active = false;
+
+ AlignmentPanel ap;
+
+ AlignViewport av;
+
+ boolean resizing = false;
+
+ int oldY, mouseX;
+
+ static String ADDNEW = "Add New Row";
+
+ static String EDITNAME = "Edit Label/Description";
+
+ static String HIDE = "Hide This Row";
+
+ static String SHOWALL = "Show All Hidden Rows";
+
+ static String OUTPUT_TEXT = "Show Values In Textbox";
+
+ static String COPYCONS_SEQ = "Copy Consensus Sequence";
+
+ int scrollOffset = 0;
+
+ int selectedRow = -1;
+
+ Tooltip tooltip;
+
+ private boolean hasHiddenRows;
+
+ public AnnotationLabels(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ this.av = ap.av;
+ setLayout(null);
+
+ /**
+ * this retrieves the adjustable height glyph from resources. we don't use
+ * it at the moment. java.net.URL url =
+ * getClass().getResource("/images/idwidth.gif"); Image temp = null;
+ *
+ * if (url != null) { temp =
+ * java.awt.Toolkit.getDefaultToolkit().createImage(url); }
+ *
+ * try { MediaTracker mt = new MediaTracker(this); mt.addImage(temp, 0);
+ * mt.waitForID(0); } catch (Exception ex) { }
+ *
+ * BufferedImage bi = new BufferedImage(temp.getHeight(this),
+ * temp.getWidth(this), BufferedImage.TYPE_INT_RGB); Graphics2D g =
+ * (Graphics2D) bi.getGraphics(); g.rotate(Math.toRadians(90));
+ * g.drawImage(temp, 0, -bi.getWidth(this), this); image = (Image) bi;
+ */
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ }
+
+ public AnnotationLabels(AlignViewport av)
+ {
+ this.av = av;
+ }
+
+ public void setScrollOffset(int y, boolean repaint)
+ {
+ scrollOffset = y;
+ if (repaint)
+ {
+ repaint();
+ }
+ }
+
+ /**
+ *
+ * @param y
+ * @return -2 if no rows are visible at all, -1 if no visible rows were
+ * selected
+ */
+ int getSelectedRow(int y)
+ {
+ int row = -2;
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+
+ if (aa == null)
+ {
+ return row;
+ }
+ int height = 0;
+ for (int i = 0; i < aa.length; i++)
+ {
+ row = -1;
+ if (!aa[i].visible)
+ {
+ continue;
+ }
+ height += aa[i].height;
+ if (y < height)
+ {
+ row = i;
+ break;
+ }
+ }
+
+ return row;
+ }
+
+ public void actionPerformed(ActionEvent evt)
+ {
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+
+ if (evt.getActionCommand().equals(ADDNEW))
+ {
+ AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null,
+ new Annotation[ap.av.getAlignment().getWidth()]);
+
+ if (!editLabelDescription(newAnnotation))
+ {
+ return;
+ }
+
+ ap.av.getAlignment().addAnnotation(newAnnotation);
+ ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
+ }
+ else if (evt.getActionCommand().equals(EDITNAME))
+ {
+ editLabelDescription(aa[selectedRow]);
+ }
+ else if (evt.getActionCommand().equals(HIDE))
+ {
+ aa[selectedRow].visible = false;
+ }
+ else if (evt.getActionCommand().equals(SHOWALL))
+ {
+ for (int i = 0; i < aa.length; i++)
+ {
+ aa[i].visible = (aa[i].annotations == null) ? false : true;
+ }
+ }
+ else if (evt.getActionCommand().equals(OUTPUT_TEXT))
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false,
+ ap.alignFrame);
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame, ap.alignFrame.getTitle()
+ + " - " + aa[selectedRow].label, 500, 100);
+ cap.setText(aa[selectedRow].toString());
+ }
+ else if (evt.getActionCommand().equals(COPYCONS_SEQ))
+ {
+ SequenceI cons = av.getConsensusSeq();
+ if (cons != null)
+ {
+ copy_annotseqtoclipboard(cons);
+ }
+
+ }
+ refresh();
+ }
+
+ /**
+ * Adjust size and repaint
+ */
+ protected void refresh()
+ {
+ ap.annotationPanel.adjustPanelHeight();
+ setSize(getSize().width, ap.annotationPanel.getSize().height);
+ ap.validate();
+ ap.paintAlignment(true);
+ }
+
+ boolean editLabelDescription(AlignmentAnnotation annotation)
+ {
+ Checkbox padGaps = new Checkbox("Fill Empty Gaps With \""
+ + ap.av.getGapCharacter() + "\"", annotation.padGaps);
+
+ EditNameDialog dialog = new EditNameDialog(annotation.label,
+ annotation.description, " Annotation Label",
+ "Annotation Description", ap.alignFrame,
+ "Edit Annotation Name / Description", 500, 180, false);
+
+ Panel empty = new Panel(new FlowLayout());
+ empty.add(padGaps);
+ dialog.add(empty);
+ dialog.pack();
+
+ dialog.setVisible(true);
+
+ if (dialog.accept)
+ {
+ annotation.label = dialog.getName();
+ annotation.description = dialog.getDescription();
+ annotation.setPadGaps(padGaps.getState(), av.getGapCharacter());
+ repaint();
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+
+ }
+
+ boolean resizePanel = false;
+
+ public void mouseMoved(MouseEvent evt)
+ {
+ resizePanel = evt.getY() < 10 && evt.getX() < 14;
+ int row = getSelectedRow(evt.getY() + scrollOffset);
+
+ if (row > -1)
+ {
+ ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(
+ av.getAlignment().getAlignmentAnnotation()[row]
+ .getDescription(true),
+ true, "\n");
+ if (tooltip == null)
+ {
+ tooltip = new Tooltip(phb.getNonHtmlContent(), this);
+ }
+ else
+ {
+ tooltip.setTip(phb.getNonHtmlContent());
+ }
+ }
+ else if (tooltip != null)
+ {
+ tooltip.setTip("");
+ }
+ }
+
+ /**
+ * curent drag position
+ */
+ MouseEvent dragEvent = null;
+
+ /**
+ * flag to indicate drag events should be ignored
+ */
+ private boolean dragCancelled = false;
+
+ /**
+ * clear any drag events in progress
+ */
+ public void cancelDrag()
+ {
+ dragEvent = null;
+ dragCancelled = true;
+ }
+
+ public void mouseDragged(MouseEvent evt)
+ {
+ if (dragCancelled)
+ {
+ return;
+ }
+ ;
+ dragEvent = evt;
+
+ if (resizePanel)
+ {
+ Dimension d = ap.annotationPanelHolder.getSize(), e = ap.annotationSpaceFillerHolder
+ .getSize(), f = ap.seqPanelHolder.getSize();
+ int dif = evt.getY() - oldY;
+
+ dif /= ap.av.getCharHeight();
+ dif *= ap.av.getCharHeight();
+
+ if ((d.height - dif) > 20 && (f.height + dif) > 20)
+ {
+ ap.annotationPanel.setSize(d.width, d.height - dif);
+ setSize(new Dimension(e.width, d.height - dif));
+ ap.annotationSpaceFillerHolder.setSize(new Dimension(e.width,
+ d.height - dif));
+ ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height
+ - dif));
+ ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
+ av.calcPanelHeight());
+ f.height += dif;
+ ap.seqPanelHolder.setPreferredSize(f);
+ ap.setScrollValues(av.getStartRes(), av.getStartSeq());
+ ap.validate();
+ // ap.paintAlignment(true);
+ ap.addNotify();
+ }
+
+ }
+ else
+ {
+ int diff;
+ if ((diff = 6 - evt.getY()) > 0)
+ {
+ // nudge scroll up
+ ap.apvscroll.setValue(ap.apvscroll.getValue() - diff);
+ ap.adjustmentValueChanged(null);
+
+ }
+ else if ((0 < (diff = 6
+ - ap.annotationSpaceFillerHolder.getSize().height
+ + evt.getY())))
+ {
+ // nudge scroll down
+ ap.apvscroll.setValue(ap.apvscroll.getValue() + diff);
+ ap.adjustmentValueChanged(null);
+ }
+ repaint();
+ }
+ }
+
+ public void mouseClicked(MouseEvent evt)
+ {
+ }
+
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (!resizePanel && !dragCancelled)
+ {
+ int start = selectedRow;
+
+ int end = getSelectedRow(evt.getY() + scrollOffset);
+
+ if (start > -1 && start != end)
+ {
+ // Swap these annotations
+ AlignmentAnnotation startAA = ap.av.getAlignment()
+ .getAlignmentAnnotation()[start];
+ if (end == -1)
+ {
+ end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
+ }
+ AlignmentAnnotation endAA = ap.av.getAlignment()
+ .getAlignmentAnnotation()[end];
+
+ ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
+ ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
+ }
+ }
+ resizePanel = false;
+ dragEvent = null;
+ dragCancelled = false;
+ repaint();
+ ap.annotationPanel.repaint();
+ }
+
+ public void mouseEntered(MouseEvent evt)
+ {
+ if (evt.getY() < 10 && evt.getX() < 14)
+ {
+ resizePanel = true;
+ repaint();
+ }
+ }
+
+ public void mouseExited(MouseEvent evt)
+ {
+ dragCancelled = false;
+
+ if (dragEvent == null)
+ {
+ resizePanel = false;
+ }
+ else
+ {
+ if (!resizePanel)
+ {
+ dragEvent = null;
+ }
+ }
+ repaint();
+ }
+
+ public void mousePressed(MouseEvent evt)
+ {
+ oldY = evt.getY();
+ if (resizePanel)
+ {
+ return;
+ }
+ dragCancelled = false;
+ // todo: move below to mouseClicked ?
+ selectedRow = getSelectedRow(evt.getY() + scrollOffset);
+
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+
+ // DETECT RIGHT MOUSE BUTTON IN AWT
+ if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ {
+
+ PopupMenu popup = new PopupMenu(
+ MessageManager.getString("label.annotations"));
+
+ MenuItem item = new MenuItem(ADDNEW);
+ item.addActionListener(this);
+ popup.add(item);
+ if (selectedRow < 0)
+ {
+ // this never happens at moment: - see comment on JAL-563
+ if (hasHiddenRows)
+ {
+ item = new MenuItem(SHOWALL);
+ item.addActionListener(this);
+ popup.add(item);
+ }
+ this.add(popup);
+ popup.show(this, evt.getX(), evt.getY());
+ return;
+ }
+ // add the rest if there are actually rows to show
+ item = new MenuItem(EDITNAME);
+ item.addActionListener(this);
+ popup.add(item);
+ item = new MenuItem(HIDE);
+ item.addActionListener(this);
+ popup.add(item);
+
+ /*
+ * Hide all