-package jalview.gui;\r
-\r
-import java.awt.*;\r
-import java.awt.Graphics2D.*;\r
-import java.awt.image.*;\r
-import javax.swing.*;\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-public class IdCanvas extends JPanel\r
-{\r
- protected AlignViewport av;\r
-\r
- protected boolean showScores = true;\r
-\r
- protected int maxIdLength = -1;\r
- protected String maxIdStr = null;\r
- BufferedImage image;\r
- Graphics2D gg;\r
- int imgHeight=0;\r
- boolean fastPaint = false;\r
-\r
- java.util.ArrayList searchResults;\r
-\r
- public IdCanvas(AlignViewport av)\r
- {\r
- setLayout(new BorderLayout());\r
- this.av = av;\r
- PaintRefresher.Register(this);\r
- }\r
-\r
- public void drawIdString(Graphics2D gg,SequenceI s,int i, int starty, int ypos) {\r
- int charHeight = av.getCharHeight();\r
-\r
- if(searchResults!=null && searchResults.contains(s))\r
- {\r
- gg.setColor(Color.black);\r
- gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight);\r
- gg.setColor(Color.white);\r
- }\r
- else if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(s)) {\r
- gg.setColor(Color.lightGray);\r
- gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight);\r
- gg.setColor(Color.white);\r
- } else {\r
- gg.setColor(s.getColor());\r
- gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight);\r
- gg.setColor(Color.black);\r
- }\r
-\r
- String string = s.getName();\r
- if(av.getShowFullId())\r
- string = s.getDisplayId();\r
-\r
- gg.drawString(string,0,AlignmentUtil.getPixelHeight(starty,i,charHeight) + ypos + charHeight- (charHeight/5));\r
-\r
- }\r
-\r
- public void fastPaint(int vertical)\r
- {\r
- if(gg==null)\r
- { repaint(); return;}\r
-\r
- gg.copyArea( 0,0, getWidth(), imgHeight, 0, -vertical*av.charHeight );\r
-\r
- int ss=av.startSeq, es=av.endSeq, transY = 0;\r
- if (vertical > 0) // scroll down\r
- {\r
- ss = es - vertical;\r
- if(ss<av.startSeq) // ie scrolling too fast, more than a page at a time\r
- ss = av.startSeq;\r
- else\r
- transY = imgHeight - vertical * av.charHeight;\r
- }\r
- else if (vertical < 0)\r
- {\r
- es = ss - vertical;\r
- if(es > av.endSeq)\r
- es = av.endSeq;\r
- }\r
-\r
-\r
-\r
- gg.translate(0, transY);\r
-\r
- drawIds(ss, es);\r
-\r
- gg.translate( 0, -transY );\r
-\r
-\r
- fastPaint = true;\r
- repaint();\r
- }\r
-\r
- public void paintComponent(Graphics g)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, getWidth(), getHeight());\r
-\r
- if (fastPaint)\r
- {\r
- fastPaint = false;\r
- g.drawImage(image, 0, 0, this);\r
- return;\r
- }\r
-\r
- imgHeight = getHeight();\r
- imgHeight -= imgHeight % av.charHeight;\r
- image = new BufferedImage(getWidth(), imgHeight, BufferedImage.TYPE_INT_RGB);\r
- gg = (Graphics2D) image.getGraphics();\r
- //Fill in the background\r
- gg.setColor(Color.white);\r
- gg.fillRect(0, 0, getWidth(), imgHeight);\r
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
- Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
- av.getFont().getSize());\r
- gg.setFont(italic);\r
-\r
- drawIds( av.getStartSeq(), av.endSeq);\r
-\r
- g.drawImage(image, 0, 0, this);\r
- }\r
-\r
- void drawIds(int starty, int endy)\r
- {\r
- Color currentColor = Color.white;\r
- Color currentTextColor = Color.black;\r
-\r
- if (av.getWrapAlignment())\r
- {\r
-\r
- int rowSize = av.getEndRes() - av.getStartRes();\r
- // Draw the rest of the panels\r
-\r
- for(int ypos=2*av.charHeight, row=av.getEndRes()-rowSize;\r
- ypos <= getHeight() && row<av.alignment.getWidth();\r
- ypos += av.chunkHeight, row+=rowSize )\r
- {\r
- for (int i = starty; i < av.alignment.getHeight(); i++)\r
- {\r
- SequenceI s = av.alignment.getSequenceAt(i);\r
- drawIdString(gg, s, i, 0, ypos);\r
- }\r
- }\r
-\r
-\r
- } else\r
- {\r
-\r
- //Now draw the id strings\r
- for (int i = starty; i < endy; i++)\r
- {\r
- // Selected sequence colours\r
-\r
- if(searchResults!=null && searchResults.contains(av.alignment.getSequenceAt(i)))\r
- {\r
- gg.setColor(Color.black);\r
- currentColor = Color.black;\r
- currentTextColor = Color.white;\r
- }\r
- else if (av.getSelectionGroup()!= null\r
- && av.getSelectionGroup().sequences.contains(av.alignment.getSequenceAt(i)))\r
- {\r
- currentColor = Color.lightGray;\r
- currentTextColor = Color.black;\r
- }\r
- else\r
- {\r
- currentColor = av.alignment.getSequenceAt(i).getColor();\r
- currentTextColor = Color.black;\r
- }\r
-\r
- gg.setColor(currentColor);\r
-\r
- gg.fillRect(0,\r
- AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
- getWidth(),\r
- av.charHeight);\r
-\r
- gg.setColor(currentTextColor);\r
- String string = av.alignment.getSequenceAt(i).getName();\r
- if(av.getShowFullId())\r
- string = av.alignment.getSequenceAt(i).getDisplayId();\r
- gg.drawString(string, 0,\r
- AlignmentUtil.getPixelHeight(starty, i, av.charHeight) +\r
- av.charHeight - (av.charHeight / 5));\r
- }\r
-\r
- // add a border\r
- gg.setColor(Color.white);\r
- gg.fillRect(getWidth()-4,0,4,getHeight());\r
- }\r
-\r
- }\r
-\r
- public void setHighlighted(java.util.ArrayList found)\r
- {\r
- searchResults = found;\r
- repaint();\r
- }\r
-}\r
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+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.beans.PropertyChangeEvent;
+import java.util.List;
+
+import javax.swing.JPanel;
+
+import jalview.datamodel.SequenceI;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdCanvas extends JPanel implements ViewportListenerI
+{
+ 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<SequenceI> searchResults;
+
+ 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());
+ av.getRanges().addPropertyChangeListener(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * 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 g, 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))
+ {
+ g.setColor(Color.black);
+ g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+ charHeight);
+ g.setColor(Color.white);
+ }
+ else if ((av.getSelectionGroup() != null)
+ && av.getSelectionGroup().getSequences(null).contains(s))
+ {
+ g.setColor(Color.lightGray);
+ g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+ charHeight);
+ g.setColor(Color.white);
+ }
+ else
+ {
+ g.setColor(av.getSequenceColour(s));
+ g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+ charHeight);
+ g.setColor(Color.black);
+ }
+
+ if (av.isRightAlignIds())
+ {
+ FontMetrics fm = g.getFontMetrics();
+ xPos = panelWidth
+ - fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4;
+ }
+
+ g.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
+ (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
+
+ if (hiddenRows && av.getShowHiddenMarkers())
+ {
+ drawMarker(g, av, i, starty, ypos);
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param vertical
+ * DOCUMENT ME!
+ */
+ public void fastPaint(int vertical)
+ {
+ /*
+ * for now, not attempting fast paint of wrapped ids...
+ */
+ if (gg == null || av.getWrapAlignment())
+ {
+ repaint();
+
+ return;
+ }
+
+ ViewportRanges ranges = av.getRanges();
+
+ gg.copyArea(0, 0, getWidth(), imgHeight, 0,
+ -vertical * av.getCharHeight());
+
+ int ss = ranges.getStartSeq();
+ int es = ranges.getEndSeq();
+ int transY = 0;
+
+ if (vertical > 0) // scroll down
+ {
+ ss = es - vertical;
+
+ if (ss < ranges.getStartSeq())
+ { // ie scrolling too fast, more than a page at a time
+ ss = ranges.getStartSeq();
+ }
+ else
+ {
+ transY = imgHeight - ((vertical + 1) * av.getCharHeight());
+ }
+ }
+ else if (vertical < 0) // scroll up
+ {
+ es = ss - vertical;
+
+ if (es > ranges.getEndSeq())
+ {
+ es = ranges.getEndSeq();
+ }
+ }
+
+ gg.translate(0, transY);
+
+ drawIds(gg, av, ss, es, searchResults);
+
+ gg.translate(0, -transY);
+
+ fastPaint = true;
+
+ // Call repaint on alignment panel so that repaints from other alignment
+ // panel components can be aggregated. Otherwise performance of the overview
+ // window and others may be adversely affected.
+ av.getAlignPanel().repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ */
+ @Override
+ public void paintComponent(Graphics g)
+ {
+ super.paintComponent(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(gg, av, av.getRanges().getStartSeq(), av.getRanges().getEndSeq(), searchResults);
+
+ g.drawImage(image, 0, 0, this);
+ }
+
+ /**
+ * Draws sequence ids from sequence index startSeq to endSeq (inclusive), with
+ * the font and other display settings configured on the viewport. Ids of
+ * sequences included in the selection are coloured grey, otherwise the
+ * current id colour for the sequence id is used.
+ *
+ * @param g
+ * @param alignViewport
+ * @param startSeq
+ * @param endSeq
+ * @param selection
+ */
+ void drawIds(Graphics2D g, AlignViewport alignViewport, final int startSeq,
+ final int endSeq, List<SequenceI> selection)
+ {
+ Font font = alignViewport.getFont();
+ if (alignViewport.isSeqNameItalics())
+ {
+ setIdfont(new Font(font.getName(), Font.ITALIC,
+ font.getSize()));
+ }
+ else
+ {
+ setIdfont(font);
+ }
+
+ g.setFont(getIdfont());
+ FontMetrics fm = g.getFontMetrics();
+
+ if (alignViewport.antiAlias)
+ {
+ g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ }
+
+ Color currentColor = Color.white;
+ Color currentTextColor = Color.black;
+
+ boolean hasHiddenRows = alignViewport.hasHiddenRows();
+
+ if (alignViewport.getWrapAlignment())
+ {
+ drawIdsWrapped(g, alignViewport, startSeq, getHeight());
+ return;
+ }
+
+ // Now draw the id strings
+ int panelWidth = getWidth();
+ int xPos = 0;
+
+ // Now draw the id strings
+ for (int i = startSeq; i <= endSeq; i++)
+ {
+ SequenceI sequence = alignViewport.getAlignment().getSequenceAt(i);
+
+ if (sequence == null)
+ {
+ continue;
+ }
+
+ if (hasHiddenRows || alignViewport.isDisplayReferenceSeq())
+ {
+ g.setFont(getHiddenFont(sequence, alignViewport));
+ fm = g.getFontMetrics();
+ }
+
+ // Selected sequence colours
+ if (selection != null && selection.contains(sequence))
+ {
+ currentColor = Color.black;
+ currentTextColor = Color.white;
+ }
+ else if ((alignViewport.getSelectionGroup() != null) && alignViewport
+ .getSelectionGroup().getSequences(null).contains(sequence))
+ {
+ currentColor = Color.lightGray;
+ currentTextColor = Color.black;
+ }
+ else
+ {
+ currentColor = alignViewport.getSequenceColour(sequence);
+ currentTextColor = Color.black;
+ }
+
+ g.setColor(currentColor);
+
+ int charHeight = alignViewport.getCharHeight();
+ g.fillRect(0, (i - startSeq) * charHeight,
+ getWidth(), charHeight);
+
+ g.setColor(currentTextColor);
+
+ String string = sequence
+ .getDisplayId(alignViewport.getShowJVSuffix());
+
+ if (alignViewport.isRightAlignIds())
+ {
+ xPos = panelWidth - fm.stringWidth(string) - 4;
+ }
+
+ g.drawString(string, xPos, (((i - startSeq) * charHeight) + charHeight)
+ - (charHeight / 5));
+
+ if (hasHiddenRows && av.getShowHiddenMarkers())
+ {
+ drawMarker(g, alignViewport, i, startSeq, 0);
+ }
+ }
+ }
+
+ /**
+ * Draws sequence ids, and annotation labels if annotations are shown, in
+ * wrapped mode
+ *
+ * @param g
+ * @param alignViewport
+ * @param startSeq
+ */
+ void drawIdsWrapped(Graphics2D g, AlignViewport alignViewport,
+ int startSeq, int pageHeight)
+ {
+ int alignmentWidth = alignViewport.getAlignment().getWidth();
+ final int alheight = alignViewport.getAlignment().getHeight();
+
+ /*
+ * assumption: SeqCanvas.calculateWrappedGeometry has been called
+ */
+ SeqCanvas seqCanvas = alignViewport.getAlignPanel()
+ .getSeqPanel().seqCanvas;
+
+ final int charHeight = alignViewport.getCharHeight();
+
+ AnnotationLabels labels = null;
+ if (alignViewport.isShowAnnotation())
+ {
+ labels = new AnnotationLabels(alignViewport);
+ }
+
+ ViewportRanges ranges = alignViewport.getRanges();
+
+ int rowSize = ranges.getViewportWidth();
+
+ /*
+ * draw repeating sequence ids until out of sequence data or
+ * out of visible space, whichever comes first
+ */
+ boolean hasHiddenRows = alignViewport.hasHiddenRows();
+ int ypos = seqCanvas.wrappedSpaceAboveAlignment;
+ int rowStartRes = ranges.getStartRes();
+ while ((ypos <= pageHeight) && (rowStartRes < alignmentWidth))
+ {
+ for (int i = startSeq; i < alheight; i++)
+ {
+ SequenceI s = alignViewport.getAlignment().getSequenceAt(i);
+ if (hasHiddenRows || alignViewport.isDisplayReferenceSeq())
+ {
+ g.setFont(getHiddenFont(s, alignViewport));
+ }
+ else
+ {
+ g.setFont(getIdfont());
+ }
+ drawIdString(g, hasHiddenRows, s, i, 0, ypos);
+ }
+
+ if (labels != null && alignViewport.isShowAnnotation())
+ {
+ g.translate(0, ypos + (alheight * charHeight));
+ labels.drawComponent(g, getWidth());
+ g.translate(0, -ypos - (alheight * charHeight));
+ }
+
+ ypos += seqCanvas.wrappedRepeatHeightPx;
+ rowStartRes += rowSize;
+ }
+ }
+
+ /**
+ * Draws a marker (a blue right-pointing triangle) between sequences to
+ * indicate hidden sequences.
+ *
+ * @param g
+ * @param alignViewport
+ * @param seqIndex
+ * @param starty
+ * @param yoffset
+ */
+ void drawMarker(Graphics2D g, AlignViewport alignViewport, int seqIndex, int starty, int yoffset)
+ {
+ SequenceI[] hseqs = alignViewport.getAlignment()
+ .getHiddenSequences().hiddenSequences;
+ // Use this method here instead of calling hiddenSeq adjust
+ // 3 times.
+ int hSize = hseqs.length;
+
+ int hiddenIndex = seqIndex;
+ int lastIndex = seqIndex - 1;
+ int nextIndex = seqIndex + 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++;
+ }
+ }
+ }
+
+ /*
+ * are we below or above the hidden sequences?
+ */
+ boolean below = (hiddenIndex > lastIndex + 1);
+ boolean above = (nextIndex > hiddenIndex + 1);
+
+ g.setColor(Color.blue);
+ int charHeight = av.getCharHeight();
+
+ /*
+ * vertices of the triangle, below or above hidden seqs
+ */
+ int[] xPoints = new int[]
+ { getWidth() - charHeight,
+ getWidth() - charHeight, getWidth() };
+ int yShift = seqIndex - starty;
+
+ if (below)
+ {
+ int[] yPoints = new int[] { yShift * charHeight + yoffset,
+ yShift * charHeight + yoffset + charHeight / 4,
+ yShift * charHeight + yoffset };
+ g.fillPolygon(xPoints, yPoints, 3);
+ }
+ if (above)
+ {
+ yShift++;
+ int[] yPoints = new int[] { yShift * charHeight + yoffset,
+ yShift * charHeight + yoffset - charHeight / 4,
+ yShift * charHeight + yoffset };
+ g.fillPolygon(xPoints, yPoints, 3);
+ }
+ }
+
+ /**
+ * Answers the standard sequence id font, or a bold font if the sequence is
+ * set as reference or a hidden group representative
+ *
+ * @param seq
+ * @param alignViewport
+ * @return
+ */
+ private Font getHiddenFont(SequenceI seq, AlignViewport alignViewport)
+ {
+ if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq))
+ {
+ return new Font(av.getFont().getName(), Font.BOLD,
+ av.getFont().getSize());
+ }
+ return getIdfont();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param list
+ * DOCUMENT ME!
+ */
+ public void setHighlighted(List<SequenceI> list)
+ {
+ searchResults = list;
+ repaint();
+ }
+
+ public Font getIdfont()
+ {
+ return idfont;
+ }
+
+ public void setIdfont(Font idfont)
+ {
+ this.idfont = idfont;
+ }
+
+ /**
+ * Respond to viewport range changes (e.g. alignment panel was scrolled). Both
+ * scrolling and resizing change viewport ranges. Scrolling changes both start
+ * and end points, but resize only changes end values. Here we only want to
+ * fastpaint on a scroll, with resize using a normal paint, so scroll events
+ * are identified as changes to the horizontal or vertical start value.
+ * <p>
+ * In unwrapped mode, only responds to a vertical scroll, as horizontal scroll
+ * leaves sequence ids unchanged. In wrapped mode, only vertical scroll is
+ * provided, but it generates a change of "startres" which does require an
+ * update here.
+ */
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ String propertyName = evt.getPropertyName();
+ if (propertyName.equals(ViewportRanges.STARTSEQ)
+ || (av.getWrapAlignment()
+ && propertyName.equals(ViewportRanges.STARTRES)))
+ {
+ fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
+ }
+ else if (propertyName.equals(ViewportRanges.STARTRESANDSEQ))
+ {
+ fastPaint(((int[]) evt.getNewValue())[1]
+ - ((int[]) evt.getOldValue())[1]);
+ }
+ else if (propertyName.equals(ViewportRanges.MOVE_VIEWPORT))
+ {
+ repaint();
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff