-package jalview.gui;\r
-\r
-import java.awt.*;\r
-import java.awt.Graphics2D.*;\r
-\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
-\r
- public IdCanvas(AlignViewport av)\r
- {\r
- setLayout(new BorderLayout());\r
- this.av = av;\r
- PaintRefresher.Register(this);\r
- }\r
-\r
- public void drawIdString(Graphics gg,SequenceI s,int i, int starty, int ypos) {\r
- int charHeight = av.getCharHeight();\r
-\r
-\r
- 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 paintComponent(Graphics gg) {\r
- AlignmentI al = av.alignment;\r
- int charHeight = av.charHeight;\r
- Font italic = new Font(av.getFont().getName(), Font.ITALIC, av.getFont().getSize());\r
-\r
- gg.setFont(italic);\r
-\r
-\r
- //Fill in the background\r
- gg.setColor(Color.white);\r
- gg.fillRect(0,0,getWidth(),getHeight());\r
-\r
- Color currentColor = Color.white;\r
- Color currentTextColor = Color.black;\r
-\r
- //Which ids are we printing\r
- int starty = av.getStartSeq();\r
- int endy = av.endSeq;\r
-\r
- if (av.getWrapAlignment())\r
- {\r
- // Draw the rest of the panels\r
- int chunkHeight = (al.getHeight() + 2)*av.charHeight;\r
- int row = av.getStartRes() / av.chunkWidth ;\r
- for(int ypos=2*av.charHeight;\r
- ypos <= getHeight() && row*av.chunkWidth<al.getWidth();\r
- ypos += chunkHeight, row++ )\r
- {\r
- for (int i = starty; i < av.alignment.getHeight(); i++)\r
- {\r
- SequenceI s = al.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 (av.getSelectionGroup()!= null && av.getSelectionGroup().sequences.contains(al.getSequenceAt(i)))\r
- {\r
- // if(av.alignment.findGroup(al.getSequenceAt(i)).getEndRes()==\r
- currentColor = Color.lightGray;\r
- currentTextColor = Color.black;\r
- }\r
- else\r
- {\r
- currentColor = al.getSequenceAt(i).getColor();\r
- currentTextColor = Color.black;\r
- }\r
-\r
- gg.setColor(currentColor);\r
-\r
- gg.fillRect(0,\r
- AlignmentUtil.getPixelHeight(starty, i, charHeight),\r
- getWidth(),\r
- charHeight);\r
-\r
- gg.setColor(currentTextColor);\r
- String string = al.getSequenceAt(i).getName();\r
- if(av.getShowFullId())\r
- string = al.getSequenceAt(i).getDisplayId();\r
- gg.drawString(string, 0,\r
- AlignmentUtil.getPixelHeight(starty, i, charHeight) +\r
- charHeight - (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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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<SequenceI> 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<SequenceI> list)
+ {
+ searchResults = list;
+ repaint();
+ }
+
+ public Font getIdfont()
+ {
+ return idfont;
+ }
+
+ public void setIdfont(Font idfont)
+ {
+ this.idfont = idfont;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff