X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=22652354d09f9aacbdb7da4aee9129bd09a824b9;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=67c3dca37b3d0036ae6e73bcad7406d9f5598bc1;hpb=51605ff0b3c81ba5894348745596b5038d905ffb;p=jalview.git
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 67c3dca..2265235 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,186 +1,513 @@
-package jalview.gui;
-
-import java.awt.*;
-import java.awt.Graphics2D.*;
-
-import javax.swing.*;
-import jalview.datamodel.*;
-import jalview.analysis.*;
-public class IdCanvas extends JPanel
-{
- protected AlignViewport av;
-
- public boolean paintFlag = false;
- protected boolean showScores = true;
-
- protected int maxIdLength = -1;
- protected String maxIdStr = null;
-
- public IdCanvas(AlignViewport av)
- {
- setLayout(new BorderLayout());
- this.av = av;
- PaintRefresher.Register(this);
- }
-
- public void drawIdString(Graphics gg,SequenceI ds,int i, int starty, int ypos) {
- int charHeight = av.getCharHeight();
-
- if (av.getSelection().contains(ds)) {
- gg.setColor(Color.gray);
- gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight);
- gg.setColor(Color.white);
- } else {
- gg.setColor(ds.getColor());
- gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight);
- gg.setColor(Color.black);
- }
-
- String string = ds.getName() + "/" + ds.getStart() + "-" + ds.getEnd();
-
- gg.drawString(string,0,AlignmentUtil.getPixelHeight(starty,i,charHeight) + ypos + charHeight- (charHeight/5));
-
- }
-
- public void paintComponent(Graphics gg) {
- AlignmentI da = av.getAlignment();
- int charHeight = av.getCharHeight();
- gg.setFont(av.getFont());
-
- //Fill in the background
- gg.setColor(Color.white);
- gg.fillRect(0,0,getWidth(),getHeight());
-
- Color currentColor = Color.white;
- Color currentTextColor = Color.black;
-
- //Which ids are we printing
- int starty = av.getStartSeq();
- int endy = av.getEndSeq();
-
- if (av.getWrapAlignment())
- {
- starty = starty%av.getChunkHeight();
-
- int ypos = 0;
- int rowstart = starty;
-
- if (starty == 0)
- ypos = 2*charHeight;
- else if (starty == 1)
- {
- starty = 0;
- ypos = charHeight;
- }
-
- endy = starty + da.getHeight();
-
- if (endy > da.getHeight()) {
- endy = da.getHeight();
- }
-
- for (int i = starty; i < endy; i++) {
- SequenceI s = da.getSequenceAt(i);
- drawIdString(gg,s,i,starty,ypos);
- }
- if (rowstart == 0) {
- ypos = ypos + av.getChunkHeight();
- } else if (rowstart == 1) {
- ypos = ypos + av.getChunkHeight();
- } else {
- ypos = ypos + av.getChunkHeight() - rowstart*charHeight;
- }
-
- starty = 0;
-
- int chunkwidth = av.getChunkWidth();
- int startx = (int)(av.getEndSeq()/chunkwidth)*chunkwidth;
- int endx = startx + chunkwidth;
-
-
- while (ypos <= getHeight() && endx < da.getWidth()) {
-
- for (int i = starty; i < endy; i++) {
- SequenceI s = da.getSequenceAt(i);
- drawIdString(gg,s,i,starty,ypos);
- }
-
- ypos += av.getChunkHeight();
- startx += chunkwidth;
- endx = startx + chunkwidth;
-
- if (endx > da.getWidth()) {
- endx = da.getWidth();
- }
-
- starty = 0;
-
- if (endy > da.getHeight()) {
- endy = da.getHeight();
- }
-
- }
- } else
- {
-
- //Now draw the id strings
- for (int i = starty; i < endy; i++)
- {
- // Selected sequence colours
- if (av.getSelection().contains(da.getSequenceAt(i)))
- {
- currentColor = Color.gray;
- currentTextColor = Color.black;
- }
- else
- {
- currentColor = da.getSequenceAt(i).getColor();
- currentTextColor = Color.black;
- }
-
- gg.setColor(currentColor);
-
- gg.fillRect(0,
- AlignmentUtil.getPixelHeight(starty, i, charHeight),
- getWidth(),
- charHeight);
-
- gg.setColor(currentTextColor);
- String string = da.getSequenceAt(i).getDisplayId();
- gg.drawString(string, 0,
- AlignmentUtil.getPixelHeight(starty, i, charHeight) +
- charHeight - (charHeight / 5));
- }
- }
-
- }
-
-
- public Dimension getLabelWidth()
- {
-
- FontMetrics fm = this.getGraphics().getFontMetrics(av.font);
- AlignmentI al = av.getAlignment();
-
- int i = 0;
- int idWidth = 0;
-
- while (i < al.getHeight() && al.getSequenceAt(i) != null)
- {
- SequenceI s = al.getSequenceAt(i);
- String str = s.getDisplayId();
- if (fm.stringWidth(str) > idWidth)
- idWidth = fm.stringWidth(str);
- i++;
- }
-
- return new Dimension(idWidth + 10,getHeight());
- }
-
- public Dimension getPreferredSize()
- {
- return getLabelWidth();
- }
-
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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.gui;
+
+import jalview.datamodel.SequenceI;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.image.BufferedImage;
+import java.util.List;
+
+import javax.swing.JPanel;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdCanvas extends JPanel
+{
+ protected AlignViewport av;
+
+ protected boolean showScores = true;
+
+ protected int maxIdLength = -1;
+
+ protected String maxIdStr = null;
+
+ BufferedImage image;
+
+ Graphics2D gg;
+
+ int imgHeight = 0;
+
+ boolean fastPaint = false;
+
+ List searchResults;
+
+ FontMetrics fm;
+
+ AnnotationLabels labels = null;
+
+ AnnotationPanel ap;
+
+ private Font idfont;
+
+ /**
+ * Creates a new IdCanvas object.
+ *
+ * @param av
+ * DOCUMENT ME!
+ */
+ public IdCanvas(AlignViewport av)
+ {
+ setLayout(new BorderLayout());
+ this.av = av;
+ PaintRefresher.Register(this, av.getSequenceSetId());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param gg
+ * DOCUMENT ME!
+ * @param hiddenRows
+ * true - check and display hidden row marker if need be
+ * @param s
+ * DOCUMENT ME!
+ * @param i
+ * DOCUMENT ME!
+ * @param starty
+ * DOCUMENT ME!
+ * @param ypos
+ * DOCUMENT ME!
+ */
+ public void drawIdString(Graphics2D gg, boolean hiddenRows, SequenceI s,
+ int i, int starty, int ypos)
+ {
+ int xPos = 0;
+ int panelWidth = getWidth();
+ int charHeight = av.getCharHeight();
+
+ if ((searchResults != null) && searchResults.contains(s))
+ {
+ gg.setColor(Color.black);
+ gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+ charHeight);
+ gg.setColor(Color.white);
+ }
+ else if ((av.getSelectionGroup() != null)
+ && av.getSelectionGroup().getSequences(null).contains(s))
+ {
+ gg.setColor(Color.lightGray);
+ gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+ charHeight);
+ gg.setColor(Color.white);
+ }
+ else
+ {
+ gg.setColor(av.getSequenceColour(s));
+ gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+ charHeight);
+ gg.setColor(Color.black);
+ }
+
+ if (av.isRightAlignIds())
+ {
+ xPos = panelWidth
+ - fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4;
+ }
+
+ gg.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
+ (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
+
+ if (hiddenRows)
+ {
+ drawMarker(i, starty, ypos);
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param vertical
+ * DOCUMENT ME!
+ */
+ public void fastPaint(int vertical)
+ {
+ if (gg == null)
+ {
+ repaint();
+
+ return;
+ }
+
+ gg.copyArea(0, 0, getWidth(), imgHeight, 0,
+ -vertical * av.getCharHeight());
+
+ int ss = av.startSeq;
+ int es = av.endSeq;
+ int transY = 0;
+
+ if (vertical > 0) // scroll down
+ {
+ ss = es - vertical;
+
+ if (ss < av.startSeq)
+ { // ie scrolling too fast, more than a page at a time
+ ss = av.startSeq;
+ }
+ else
+ {
+ transY = imgHeight - (vertical * av.getCharHeight());
+ }
+ }
+ else if (vertical < 0)
+ {
+ es = ss - vertical;
+
+ if (es > av.endSeq)
+ {
+ es = av.endSeq;
+ }
+ }
+
+ gg.translate(0, transY);
+
+ drawIds(ss, es);
+
+ gg.translate(0, -transY);
+
+ fastPaint = true;
+ repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ */
+ public void paintComponent(Graphics g)
+ {
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getWidth(), getHeight());
+
+ if (fastPaint)
+ {
+ fastPaint = false;
+ g.drawImage(image, 0, 0, this);
+
+ return;
+ }
+
+ int oldHeight = imgHeight;
+
+ imgHeight = getHeight();
+ imgHeight -= (imgHeight % av.getCharHeight());
+
+ if (imgHeight < 1)
+ {
+ return;
+ }
+
+ if (oldHeight != imgHeight || image.getWidth(this) != getWidth())
+ {
+ image = new BufferedImage(getWidth(), imgHeight,
+ BufferedImage.TYPE_INT_RGB);
+ }
+
+ gg = (Graphics2D) image.getGraphics();
+
+ // Fill in the background
+ gg.setColor(Color.white);
+ gg.fillRect(0, 0, getWidth(), imgHeight);
+
+ drawIds(av.getStartSeq(), av.endSeq);
+
+ g.drawImage(image, 0, 0, this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param starty
+ * DOCUMENT ME!
+ * @param endy
+ * DOCUMENT ME!
+ */
+ void drawIds(int starty, int endy)
+ {
+ if (av.isSeqNameItalics())
+ {
+ setIdfont(new Font(av.getFont().getName(), Font.ITALIC, av.getFont()
+ .getSize()));
+ }
+ else
+ {
+ setIdfont(av.getFont());
+ }
+
+ gg.setFont(getIdfont());
+ fm = gg.getFontMetrics();
+
+ if (av.antiAlias)
+ {
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ }
+
+ Color currentColor = Color.white;
+ Color currentTextColor = Color.black;
+
+ final boolean doHiddenCheck = av.isDisplayReferenceSeq()
+ || av.hasHiddenRows(), hiddenRows = av.hasHiddenRows();
+
+ if (av.getWrapAlignment())
+ {
+ int maxwidth = av.getAlignment().getWidth();
+ int alheight = av.getAlignment().getHeight();
+
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ }
+
+ int annotationHeight = 0;
+
+ if (av.isShowAnnotation())
+ {
+ if (ap == null)
+ {
+ ap = new AnnotationPanel(av);
+ }
+
+ annotationHeight = ap.adjustPanelHeight();
+ if (labels == null)
+ {
+ labels = new AnnotationLabels(av);
+ }
+ }
+
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
+ {
+ hgap += av.getCharHeight();
+ }
+
+ int cHeight = alheight * av.getCharHeight() + hgap + annotationHeight;
+
+ int rowSize = av.getEndRes() - av.getStartRes();
+
+ // Draw the rest of the panels
+ for (int ypos = hgap, row = av.startRes; (ypos <= getHeight())
+ && (row < maxwidth); ypos += cHeight, row += rowSize)
+ {
+ for (int i = starty; i < alheight; i++)
+ {
+ SequenceI s = av.getAlignment().getSequenceAt(i);
+ if (doHiddenCheck)
+ {
+ setHiddenFont(s);
+ }
+ else
+ {
+ gg.setFont(getIdfont());
+ }
+
+ drawIdString(gg, hiddenRows, s, i, 0, ypos);
+ }
+
+ if (labels != null && av.isShowAnnotation())
+ {
+ gg.translate(0, ypos + (alheight * av.getCharHeight()));
+ labels.drawComponent(gg, getWidth());
+ gg.translate(0, -ypos - (alheight * av.getCharHeight()));
+ }
+ }
+ }
+ else
+ {
+ // No need to hang on to labels if we're not wrapped
+ labels = null;
+
+ // Now draw the id strings
+ int panelWidth = getWidth();
+ int xPos = 0;
+
+ SequenceI sequence;
+ // Now draw the id strings
+ for (int i = starty; i < endy; i++)
+ {
+ sequence = av.getAlignment().getSequenceAt(i);
+
+ if (sequence == null)
+ {
+ continue;
+ }
+
+ if (doHiddenCheck)
+ {
+ setHiddenFont(sequence);
+ }
+
+ // Selected sequence colours
+ if ((searchResults != null) && searchResults.contains(sequence))
+ {
+ currentColor = Color.black;
+ currentTextColor = Color.white;
+ }
+ else if ((av.getSelectionGroup() != null)
+ && av.getSelectionGroup().getSequences(null)
+ .contains(sequence))
+ {
+ currentColor = Color.lightGray;
+ currentTextColor = Color.black;
+ }
+ else
+ {
+ currentColor = av.getSequenceColour(sequence);
+ currentTextColor = Color.black;
+ }
+
+ gg.setColor(currentColor);
+
+ gg.fillRect(0, (i - starty) * av.getCharHeight(), getWidth(),
+ av.getCharHeight());
+
+ gg.setColor(currentTextColor);
+
+ String string = sequence.getDisplayId(av.getShowJVSuffix());
+
+ if (av.isRightAlignIds())
+ {
+ xPos = panelWidth - fm.stringWidth(string) - 4;
+ }
+
+ gg.drawString(string, xPos,
+ (((i - starty) * av.getCharHeight()) + av.getCharHeight())
+ - (av.getCharHeight() / 5));
+
+ if (hiddenRows)
+ {
+ drawMarker(i, starty, 0);
+ }
+
+ }
+
+ }
+ }
+
+ void drawMarker(int i, int starty, int yoffset)
+ {
+
+ SequenceI[] hseqs = av.getAlignment().getHiddenSequences().hiddenSequences;
+ // Use this method here instead of calling hiddenSeq adjust
+ // 3 times.
+ int hSize = hseqs.length;
+
+ int hiddenIndex = i;
+ int lastIndex = i - 1;
+ int nextIndex = i + 1;
+
+ for (int j = 0; j < hSize; j++)
+ {
+ if (hseqs[j] != null)
+ {
+ if (j - 1 < hiddenIndex)
+ {
+ hiddenIndex++;
+ }
+ if (j - 1 < lastIndex)
+ {
+ lastIndex++;
+ }
+ if (j - 1 < nextIndex)
+ {
+ nextIndex++;
+ }
+ }
+ }
+
+ boolean below = (hiddenIndex > lastIndex + 1);
+ boolean above = (nextIndex > hiddenIndex + 1);
+
+ gg.setColor(Color.blue);
+ if (below)
+ {
+ gg.fillPolygon(
+ new int[] { getWidth() - av.getCharHeight(),
+ getWidth() - av.getCharHeight(), getWidth() },
+ new int[] {
+ (i - starty) * av.getCharHeight() + yoffset,
+ (i - starty) * av.getCharHeight() + yoffset
+ + av.getCharHeight() / 4,
+ (i - starty) * av.getCharHeight() + yoffset }, 3);
+ }
+ if (above)
+ {
+ gg.fillPolygon(
+ new int[] { getWidth() - av.getCharHeight(),
+ getWidth() - av.getCharHeight(), getWidth() },
+ new int[] {
+ (i - starty + 1) * av.getCharHeight() + yoffset,
+ (i - starty + 1) * av.getCharHeight() + yoffset
+ - av.getCharHeight() / 4,
+ (i - starty + 1) * av.getCharHeight() + yoffset }, 3);
+
+ }
+ }
+
+ void setHiddenFont(SequenceI seq)
+ {
+ Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
+ .getSize());
+
+ if (av.isHiddenRepSequence(seq))
+ {
+ gg.setFont(bold);
+ }
+ else
+ {
+ gg.setFont(getIdfont());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param list
+ * DOCUMENT ME!
+ */
+ public void setHighlighted(List list)
+ {
+ searchResults = list;
+ repaint();
+ }
+
+ public Font getIdfont()
+ {
+ return idfont;
+ }
+
+ public void setIdfont(Font idfont)
+ {
+ this.idfont = idfont;
+ }
+}