X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=190682941a129aca2ff76b5377fa7860c4c803a1;hb=9876fdccf311378e690c1f9e18db52675d427b89;hp=78e545aab48e720aef0b3eb2c9ec3d0dfef00a00;hpb=734927d0150e9d43593e5a2aea1fc06613a9d873;p=jalview.git
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
old mode 100755
new mode 100644
index 78e545a..1906829
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,1040 +1,1802 @@
-/*
- * 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 jalview.datamodel.*;
-
-import jalview.jbgui.*;
-
-import jalview.schemes.*;
-
-import org.jibble.epsgraphics.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import java.awt.print.*;
-
-import java.io.*;
-
-import javax.imageio.*;
-
-import javax.swing.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class AlignmentPanel extends GAlignmentPanel
- implements AdjustmentListener, Printable
-{
- AlignViewport av;
- OverviewPanel overviewPanel;
- SeqPanel seqPanel;
- IdPanel idPanel;
- IdwidthAdjuster idwidthAdjuster;
-
- /** DOCUMENT ME!! */
- public AlignFrame alignFrame;
- ScalePanel scalePanel;
- AnnotationPanel annotationPanel;
- AnnotationLabels alabels;
-
- // this value is set false when selection area being dragged
- boolean fastPaint = true;
- int hextent = 0;
- int vextent = 0;
-
- /**
- * Creates a new AlignmentPanel object.
- *
- * @param af DOCUMENT ME!
- * @param av DOCUMENT ME!
- */
- public AlignmentPanel(AlignFrame af, final AlignViewport av)
- {
- alignFrame = af;
- this.av = av;
- seqPanel = new SeqPanel(av, this);
- idPanel = new IdPanel(av, this);
-
- scalePanel = new ScalePanel(av, this);
-
- idPanelHolder.add(idPanel, BorderLayout.CENTER);
- idwidthAdjuster = new IdwidthAdjuster(this);
- idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
-
- annotationPanel = new AnnotationPanel(this);
- alabels = new AnnotationLabels(this);
-
- annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());
- annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
- annotationScroller.setViewportView(annotationPanel);
- annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
-
- fontChanged();
-
- scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
- seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
-
- setScrollValues(0, 0);
-
- hscroll.addAdjustmentListener(this);
- vscroll.addAdjustmentListener(this);
-
- setFocusable(true);
- addKeyListener(new KeyAdapter()
- {
- public void keyPressed(KeyEvent evt)
- {
- switch (evt.getKeyCode())
- {
- case 27: // escape key
- av.setSelectionGroup(null);
- repaint();
-
- break;
-
- case KeyEvent.VK_DOWN:
- alignFrame.moveSelectedSequences(false);
-
- break;
-
- case KeyEvent.VK_UP:
- alignFrame.moveSelectedSequences(true);
-
- break;
-
- case KeyEvent.VK_BACK_SPACE:
- case KeyEvent.VK_DELETE:
- alignFrame.cut_actionPerformed(null);
- break;
- }
-
- }
- });
- }
-
- /**
- * DOCUMENT ME!
- */
- public void fontChanged()
- {
- // set idCanvas bufferedImage to null
- // to prevent drawing old image
- FontMetrics fm = getFontMetrics(av.getFont());
-
- scalePanelHolder.setPreferredSize(new Dimension(10,
- av.charHeight + fm.getDescent()));
- idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
- av.charHeight + fm.getDescent()));
-
- idPanel.idCanvas.gg = null;
- seqPanel.seqCanvas.img = null;
- annotationPanel.adjustPanelHeight();
-
- Dimension d = calculateIdWidth();
- d.setSize(d.width + 4, d.height);
- idPanel.idCanvas.setPreferredSize(d);
- hscrollFillerPanel.setPreferredSize(d);
-
- if (av.getWrapAlignment())
- {
- int max = av.alignment.getWidth() /
- seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
- vscroll.setMaximum(max);
- vscroll.setUnitIncrement(1);
- vscroll.setVisibleAmount(1);
- }
- else
- {
- setScrollValues(av.getStartRes(), av.getStartSeq());
- }
-
- if(overviewPanel!=null)
- overviewPanel.updateOverviewImage();
-
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Dimension calculateIdWidth()
- {
- Container c = new Container();
-
- FontMetrics fm = c.getFontMetrics(av.font);
- AlignmentI al = av.getAlignment();
-
- int i = 0;
- int idWidth = 0;
- String id;
-
- while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
- {
- SequenceI s = al.getSequenceAt(i);
-
- if (av.getShowFullId())
- {
- id = s.getDisplayId();
- }
- else
- {
- id = s.getName();
- }
-
- if (fm.stringWidth(id) > idWidth)
- {
- idWidth = fm.stringWidth(id);
- }
-
- i++;
- }
-
- // Also check annotation label widths
- i = 0;
-
- if (al.getAlignmentAnnotation() != null)
- {
- fm = c.getFontMetrics(alabels.getFont());
-
- while (i < al.getAlignmentAnnotation().length)
- {
- String label = al.getAlignmentAnnotation()[i].label;
-
- if (fm.stringWidth(label) > idWidth)
- {
- idWidth = fm.stringWidth(label);
- }
-
- i++;
- }
- }
-
- return new Dimension(idWidth, 12);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param results DOCUMENT ME!
- */
- public void highlightSearchResults(int[] results)
- {
- seqPanel.seqCanvas.highlightSearchResults(results);
-
- // do we need to scroll the panel?
- if (results != null)
- {
- SequenceI seq = av.alignment.getSequenceAt(results[0]);
- int start = seq.findIndex(results[1]) - 1;
- int end = seq.findIndex(results[2]) - 1;
-
- if ((av.getStartRes() > start) || (av.getEndRes() < end) ||
- ((av.getStartSeq() > results[0]) ||
- (av.getEndSeq() < results[0])))
- {
- setScrollValues(start, results[0]);
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public OverviewPanel getOverviewPanel()
- {
- return overviewPanel;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param op DOCUMENT ME!
- */
- public void setOverviewPanel(OverviewPanel op)
- {
- overviewPanel = op;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- public void setAnnotationVisible(boolean b)
- {
- annotationSpaceFillerHolder.setVisible(b);
- annotationScroller.setVisible(b);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param wrap DOCUMENT ME!
- */
- public void setWrapAlignment(boolean wrap)
- {
- scalePanelHolder.setVisible(!wrap);
- hscroll.setVisible(!wrap);
- idwidthAdjuster.setVisible(!wrap);
-
- av.setShowAnnotation(!wrap);
- annotationScroller.setVisible(!wrap);
- annotationSpaceFillerHolder.setVisible(!wrap);
- idSpaceFillerPanel1.setVisible(!wrap);
-
- repaint();
- }
-
-
- // return value is true if the scroll is valid
- public boolean scrollUp(boolean up)
- {
- if (up)
- {
- if (vscroll.getValue() < 1)
- {
- return false;
- }
-
- fastPaint = false;
- vscroll.setValue(vscroll.getValue() - 1);
- }
- else
- {
- if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
- {
- return false;
- }
-
- fastPaint = false;
- vscroll.setValue(vscroll.getValue() + 1);
- }
-
- fastPaint = true;
-
- return true;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param right DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean scrollRight(boolean right)
- {
- if (right)
- {
- if (hscroll.getValue() < 1)
- {
- return false;
- }
-
- fastPaint = false;
- hscroll.setValue(hscroll.getValue() - 1);
- }
- else
- {
- if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
- {
- return false;
- }
-
- fastPaint = false;
- hscroll.setValue(hscroll.getValue() + 1);
- }
-
- fastPaint = true;
-
- return true;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param x DOCUMENT ME!
- * @param y DOCUMENT ME!
- */
- public void setScrollValues(int x, int y)
- {
- av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -
- 1);
-
- hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
- vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
-
- if (hextent > av.alignment.getWidth())
- {
- hextent = av.alignment.getWidth();
- }
-
- if (vextent > av.alignment.getHeight())
- {
- vextent = av.alignment.getHeight();
- }
-
- if ((hextent + x) > av.getAlignment().getWidth())
- {
- x = av.getAlignment().getWidth() - hextent;
- }
-
- if ((vextent + y) > av.getAlignment().getHeight())
- {
- y = av.getAlignment().getHeight() - vextent;
- }
-
- if (y < 0)
- {
- y = 0;
- }
-
- if (x < 0)
- {
- x = 0;
- }
-
- hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
- vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
- }
-
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void adjustmentValueChanged(AdjustmentEvent evt)
- {
- int oldX = av.getStartRes();
- int oldY = av.getStartSeq();
-
- if (evt.getSource() == hscroll)
- {
- int x = hscroll.getValue();
- av.setStartRes(x);
- av.setEndRes((x +
- (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
- }
-
- if (evt.getSource() == vscroll)
- {
- int offy = vscroll.getValue();
-
- if (av.getWrapAlignment())
- {
- int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
- av.setStartRes(vscroll.getValue() * rowSize);
- av.setEndRes((vscroll.getValue() + 1) * rowSize);
- }
- else
- {
- av.setStartSeq(offy);
- av.setEndSeq(offy +
- (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
- }
- }
-
- if (overviewPanel != null)
- {
- overviewPanel.setBoxPosition();
- }
-
- if (av.getWrapAlignment() || !fastPaint)
- {
- repaint();
- }
- else
- {
- idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
- seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
- av.getStartSeq() - oldY);
-
- scalePanel.repaint();
-
- if (av.getShowAnnotation())
- {
- annotationPanel.fastPaint(av.getStartRes() - oldX);
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- */
- public void paintComponent(Graphics g)
- {
- invalidate();
-
- Dimension d = idPanel.idCanvas.getPreferredSize();
- idPanelHolder.setPreferredSize(d);
- hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
- validate();
-
- if (av.getWrapAlignment())
- {
- int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
- vscroll.setMaximum(max);
- vscroll.setUnitIncrement(1);
- vscroll.setVisibleAmount(1);
- }
- else
- {
- setScrollValues(av.getStartRes(), av.getStartSeq());
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param pg DOCUMENT ME!
- * @param pf DOCUMENT ME!
- * @param pi DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- *
- * @throws PrinterException DOCUMENT ME!
- */
- public int print(Graphics pg, PageFormat pf, int pi)
- throws PrinterException
- {
- pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
-
- int pwidth = (int) pf.getImageableWidth();
- int pheight = (int) pf.getImageableHeight();
-
- if (av.getWrapAlignment())
- {
- return printWrappedAlignment(pg, pwidth, pheight, pi);
- }
- else
- {
- return printUnwrapped(pg, pwidth, pheight, pi);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param pg DOCUMENT ME!
- * @param pwidth DOCUMENT ME!
- * @param pheight DOCUMENT ME!
- * @param pi DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- *
- * @throws PrinterException DOCUMENT ME!
- */
- public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
- throws PrinterException
- {
- int idWidth = calculateIdWidth().width + 4;
- FontMetrics fm = getFontMetrics(av.getFont());
- int scaleHeight = av.charHeight + fm.getDescent();
-
- pg.setColor(Color.white);
- pg.fillRect(0, 0, pwidth, pheight);
- pg.setFont(av.getFont());
-
- ////////////////////////////////////
- /// How many sequences and residues can we fit on a printable page?
- int totalRes = (pwidth - idWidth) / av.getCharWidth();
-
- int totalSeq = (int) ((pheight - scaleHeight) / av.getCharHeight()) -
- 1;
-
- int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
-
- /////////////////////////////
- /// Only print these sequences and residues on this page
- int startRes;
-
- /////////////////////////////
- /// Only print these sequences and residues on this page
- int endRes;
-
- /////////////////////////////
- /// Only print these sequences and residues on this page
- int startSeq;
-
- /////////////////////////////
- /// Only print these sequences and residues on this page
- int endSeq;
- startRes = (pi % pagesWide) * totalRes;
- endRes = (startRes + totalRes) - 1;
-
- if (endRes > (av.getAlignment().getWidth() - 1))
- {
- endRes = av.getAlignment().getWidth() - 1;
- }
-
- startSeq = (pi / pagesWide) * totalSeq;
- endSeq = startSeq + totalSeq;
-
- if (endSeq > av.getAlignment().getHeight())
- {
- endSeq = av.getAlignment().getHeight();
- }
-
- int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight;
-
- if (av.showAnnotation)
- {
- pagesHigh += annotationPanel.getHeight();
- }
-
- pagesHigh /= pheight;
-
- if (pi >= (pagesWide * pagesHigh))
- {
- return Printable.NO_SUCH_PAGE;
- }
-
- //draw Scale
- pg.translate(idWidth, 0);
- scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
- pg.translate(-idWidth, scaleHeight);
-
- ////////////////
- // Draw the ids
- Color currentColor = null;
- Color currentTextColor = null;
-
- for (int i = startSeq; i < endSeq; i++)
- {
- if ((av.getSelectionGroup() != null) &&
- av.getSelectionGroup().sequences.contains(
- av.getAlignment().getSequenceAt(i)))
- {
- currentColor = Color.gray;
- currentTextColor = Color.black;
- }
- else
- {
- currentColor = av.getAlignment().getSequenceAt(i).getColor();
- currentTextColor = Color.black;
- }
-
- pg.setColor(currentColor);
- pg.fillRect(0, (i-startSeq) * av.charHeight, idWidth,
- av.getCharHeight());
-
- pg.setColor(currentTextColor);
-
- String string = av.getAlignment().getSequenceAt(i).getName();
-
- if (av.getShowFullId())
- {
- string = av.getAlignment().getSequenceAt(i).getDisplayId();
- }
-
- pg.drawString(string, 0,
- (((i-startSeq) * av.charHeight) + av.getCharHeight()) -
- (av.getCharHeight() / 5));
- }
-
- // draw main sequence panel
- pg.translate(idWidth, 0);
- seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,
- startRes, startSeq, 0);
-
- if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
- {
- pg.translate(-idWidth, (endSeq - startSeq) * av.charHeight);
- alabels.drawComponent((Graphics2D) pg);
- pg.translate(idWidth, 0);
- annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes +
- 1);
- }
-
- return Printable.PAGE_EXISTS;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param pg DOCUMENT ME!
- * @param pwidth DOCUMENT ME!
- * @param pheight DOCUMENT ME!
- * @param pi DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- *
- * @throws PrinterException DOCUMENT ME!
- */
- public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
- int pi) throws PrinterException
- {
- int idWidth = calculateIdWidth().width + 4;
-
- int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
- idWidth);
- int totalHeight = totalHeight = (av.alignment.getHeight() + 2) * ((av.alignment.getWidth() / resWidth) +
- 1) * av.charHeight;
-
- pg.setColor(Color.white);
- pg.fillRect(0, 0, pwidth, pheight);
- pg.setFont(av.getFont());
-
- ////////////////
- // Draw the ids
- pg.setColor(Color.black);
-
- pg.translate(0, -pi * pheight);
-
- pg.setClip(0, pi * pheight, pwidth, pheight);
-
- int ypos = 2 * av.charHeight;
-
- do
- {
- for (int i = 0; i < av.alignment.getHeight(); i++)
- {
- SequenceI s = av.alignment.getSequenceAt(i);
- String string = s.getName();
-
- if (av.getShowFullId())
- {
- string = s.getDisplayId();
- }
-
- pg.drawString(string, 0,
- ((i * av.charHeight) + ypos + av.charHeight) -
- (av.charHeight / 5));
- }
-
- ypos += ((av.alignment.getHeight() + 2) * av.charHeight);
- }
- while (ypos < totalHeight);
-
- pg.translate(idWidth, 0);
-
- seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
-
- if ((pi * pheight) < totalHeight)
- {
- return Printable.PAGE_EXISTS;
- }
- else
- {
- return Printable.NO_SUCH_PAGE;
- }
- }
-
- /**
- * DOCUMENT ME!
- */
- public void makeEPS(File epsFile)
- {
- if(epsFile == null)
- {
- jalview.io.JalviewFileChooser chooser = new jalview.io.
- JalviewFileChooser(jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"), new String[]
- {"eps"},
- new String[]
- {"Encapsulated Postscript"},
- "Encapsulated Postscript");
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Create EPS file from alignment");
- chooser.setToolTipText("Save");
-
- int value = chooser.showSaveDialog(this);
-
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
- {
- return;
- }
-
- epsFile = chooser.getSelectedFile();
-
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
- }
-
- int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
- int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
-
- if (av.getWrapAlignment())
- {
- height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
- av.chunkHeight;
- width = seqPanel.getWidth() + idPanel.getWidth();
-
- }
-
-
- if (av.getShowAnnotation())
- {
- height += annotationPanel.getPreferredSize().height;
- }
-
- try
- {
- FileOutputStream out = new FileOutputStream(epsFile);
- EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width,
- height);
-
- if (av.getWrapAlignment())
- {
- printWrappedAlignment(pg, width, height, 0);
- }
- else
- {
- printUnwrapped(pg, width, height, 0);
- }
-
- pg.flush();
- pg.close();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
-
- public void makePNGImageMap(File imgMapFile, String imageName)
- {
- ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
- //////////////////////////////////////////////
- int idWidth = calculateIdWidth().width + 4;
- FontMetrics fm = getFontMetrics(av.getFont());
- int scaleHeight = av.charHeight + fm.getDescent();
-
- // Gen image map
- //////////////////////////////////
- if(imgMapFile!=null)
- {
- try
- {
- PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
- out.println(jalview.io.HTMLOutput.getImageMapHTML());
- out.println("
"
- +"