X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=91b23e499b6e24e780e79e4f19a57118407f2b7a;hb=9493ac8f3b6a02d3cf9747ed6c0d6cf407d284e8;hp=5959493fa0cbe6b739a33b9907378dddd310eabb;hpb=628a29c56cc280f434f3568f3bf79555e1c77726;p=jalview.git
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 5959493..91b23e4 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,390 +1,492 @@
-/*
- * 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 java.awt.*;
-import java.awt.image.*;
-
-import javax.swing.*;
-
-
-/**
- * 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;
- java.util.Vector searchResults;
-
- /**
- * Creates a new IdCanvas object.
- *
- * @param av DOCUMENT ME!
- */
- public IdCanvas(AlignViewport av)
- {
- setLayout(new BorderLayout());
- this.av = av;
- PaintRefresher.Register(this, av.alignment);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param gg DOCUMENT ME!
- * @param s DOCUMENT ME!
- * @param i DOCUMENT ME!
- * @param starty DOCUMENT ME!
- * @param ypos DOCUMENT ME!
- */
- public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty, int ypos)
- {
- int charHeight = av.charHeight;
-
- 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(false).contains(s))
- {
- gg.setColor(Color.lightGray);
- gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
- charHeight);
- gg.setColor(Color.white);
- }
- else
- {
- gg.setColor(s.getColor());
- gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
- charHeight);
- gg.setColor(Color.black);
- }
-
-
- gg.drawString( s.getDisplayId(av.getShowJVSuffix()),
- 0, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
-
- if (av.hasHiddenRows && av.showHiddenMarkers)
- 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.charHeight);
-
- 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.charHeight);
- }
- }
- 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;
- }
-
- imgHeight = getHeight();
- imgHeight -= (imgHeight % av.charHeight);
-
- if (imgHeight < 1)
- {
- return;
- }
-
- 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)
- {
- Font italic = new Font(av.getFont().getName(), Font.ITALIC,
- av.getFont().getSize());
-
- gg.setFont(italic);
-
- if (av.antiAlias)
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
-
- Color currentColor = Color.white;
- Color currentTextColor = Color.black;
-
- if (av.getWrapAlignment())
- {
- int maxwidth = av.alignment.getWidth();
- int alheight = av.alignment.getHeight();
-
- if (av.hasHiddenColumns)
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
-
- int annotationHeight = 0;
- AnnotationLabels labels = null;
-
- if(av.showAnnotation)
- {
- AnnotationPanel ap = new AnnotationPanel(av);
- annotationHeight = ap.adjustPanelHeight();
- labels = new AnnotationLabels(av);
- }
-
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
- hgap += av.charHeight;
-
- int cHeight = alheight * av.charHeight
- + 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++)
- {
- if (av.hasHiddenRows)
- {
- setHiddenFont(i);
- }
- else
- gg.setFont(italic);
-
- SequenceI s = av.alignment.getSequenceAt(i);
- drawIdString(gg, s, i, 0, ypos);
- }
-
- if(labels!=null)
- {
- gg.translate(0, ypos+(alheight * av.charHeight));
- labels.drawComponent(gg, getWidth());
- gg.translate(0, -ypos-(alheight * av.charHeight));
- }
-
-
- }
- }
- else
- {
- //Now draw the id strings
-
- //Now draw the id strings
- for (int i = starty; i < endy; i++)
- {
- if (av.hasHiddenRows)
- {
- setHiddenFont(i);
- }
-
- // Selected sequence colours
- if ( (searchResults != null) &&
- searchResults.contains(av.alignment.getSequenceAt(i)))
- {
- currentColor = Color.black;
- currentTextColor = Color.white;
- }
- else if ( (av.getSelectionGroup() != null) &&
- av.getSelectionGroup().getSequences(false).contains(
- av.alignment.getSequenceAt(i)))
- {
- currentColor = Color.lightGray;
- currentTextColor = Color.black;
- }
- else
- {
- currentColor = av.alignment.getSequenceAt(i).getColor();
- currentTextColor = Color.black;
- }
-
- gg.setColor(currentColor);
-
- gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),
- av.charHeight);
-
- gg.setColor(currentTextColor);
-
- String string = av.alignment.getSequenceAt(i).getDisplayId( av.getShowJVSuffix());
-
- gg.drawString(string, 0,
- (((i - starty) * av.charHeight) + av.charHeight) -
- (av.charHeight / 5));
-
- if(av.hasHiddenRows && av.showHiddenMarkers)
- drawMarker(i, starty, 0);
-
- }
-
- }
- }
-
- void drawMarker(int i, int starty, int yoffset)
- {
- int hiddenIndex = av.adjustForHiddenSeqs(i);
- int lastIndex = av.adjustForHiddenSeqs(i - 1);
- int nextIndex = av.adjustForHiddenSeqs(i + 1);
-
- boolean below = (hiddenIndex > lastIndex + 1);
- boolean above = (nextIndex>hiddenIndex+1);
-
- gg.setColor(Color.blue);
- if(below)
- {
- gg.fillPolygon(new int[]
- {getWidth()- av.charHeight,
- getWidth()- av.charHeight,
- getWidth()},
- new int[]
- {
- (i - starty) * av.charHeight +yoffset,
- (i - starty) * av.charHeight +yoffset+ av.charHeight / 4,
- (i - starty) * av.charHeight+yoffset
- }, 3);
- }
- if(above)
- {
- gg.fillPolygon(new int[]
- {getWidth()- av.charHeight,
- getWidth()- av.charHeight,
- getWidth() },
- new int[]
- {
- (i - starty+1) * av.charHeight +yoffset,
- (i - starty+1) * av.charHeight +yoffset- av.charHeight / 4,
- (i - starty+1) * av.charHeight +yoffset
- }, 3);
-
- }
- }
-
- void setHiddenFont(int i)
- {
- Font italic = new Font(av.getFont().getName(), Font.ITALIC,
- av.getFont().getSize());
- Font bold = new Font(av.getFont().getName(), Font.BOLD,
- av.getFont().getSize());
-
- if (av.alignment.getSequenceAt(i).getHiddenSequences() != null)
- gg.setFont(bold);
- else
- gg.setFont(italic);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param found DOCUMENT ME!
- */
- public void setHighlighted(java.util.Vector found)
- {
- searchResults = found;
- repaint();
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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 java.awt.*;
+import java.awt.image.*;
+import java.util.List;
+
+import javax.swing.*;
+
+import jalview.datamodel.*;
+
+/**
+ * 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;
+
+ 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 s
+ * DOCUMENT ME!
+ * @param i
+ * DOCUMENT ME!
+ * @param starty
+ * DOCUMENT ME!
+ * @param ypos
+ * DOCUMENT ME!
+ */
+ public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,
+ int ypos)
+ {
+ int xPos = 0;
+ int panelWidth = getWidth();
+ int charHeight = av.charHeight;
+
+ 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.rightAlignIds)
+ {
+ xPos = panelWidth
+ - fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4;
+ }
+
+ gg.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
+ (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
+
+ if (av.hasHiddenRows() && av.showHiddenMarkers)
+ {
+ 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.charHeight);
+
+ 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.charHeight);
+ }
+ }
+ 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.charHeight);
+
+ 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.seqNameItalics)
+ {
+ idfont = new Font(av.getFont().getName(), Font.ITALIC, av.getFont()
+ .getSize());
+ }
+ else
+ {
+ idfont = av.getFont();
+ }
+
+ gg.setFont(idfont);
+ fm = gg.getFontMetrics();
+
+ if (av.antiAlias)
+ {
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ }
+
+ Color currentColor = Color.white;
+ Color currentTextColor = Color.black;
+
+ 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.showAnnotation)
+ {
+ if (ap == null)
+ {
+ ap = new AnnotationPanel(av);
+ }
+
+ annotationHeight = ap.adjustPanelHeight();
+ if (labels == null)
+ {
+ labels = new AnnotationLabels(av);
+ }
+ }
+
+ int hgap = av.charHeight;
+ if (av.scaleAboveWrapped)
+ {
+ hgap += av.charHeight;
+ }
+
+ int cHeight = alheight * av.charHeight + 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 (av.hasHiddenRows())
+ {
+ setHiddenFont(s);
+ }
+ else
+ {
+ gg.setFont(idfont);
+ }
+
+ drawIdString(gg, s, i, 0, ypos);
+ }
+
+ if (labels != null && av.showAnnotation)
+ {
+ gg.translate(0, ypos + (alheight * av.charHeight));
+ labels.drawComponent(gg, getWidth());
+ gg.translate(0, -ypos - (alheight * av.charHeight));
+ }
+ }
+ }
+ 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 (av.hasHiddenRows())
+ {
+ 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.charHeight, getWidth(),
+ av.charHeight);
+
+ gg.setColor(currentTextColor);
+
+ String string = sequence.getDisplayId(av.getShowJVSuffix());
+
+ if (av.rightAlignIds)
+ {
+ xPos = panelWidth - fm.stringWidth(string) - 4;
+ }
+
+ gg.drawString(string, xPos,
+ (((i - starty) * av.charHeight) + av.charHeight)
+ - (av.charHeight / 5));
+
+ if (av.hasHiddenRows() && av.showHiddenMarkers)
+ {
+ 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.charHeight, getWidth() - av.charHeight,
+ getWidth() }, new int[]
+ {
+ (i - starty) * av.charHeight + yoffset,
+ (i - starty) * av.charHeight + yoffset + av.charHeight
+ / 4, (i - starty) * av.charHeight + yoffset }, 3);
+ }
+ if (above)
+ {
+ gg.fillPolygon(
+ new int[]
+ { getWidth() - av.charHeight, getWidth() - av.charHeight,
+ getWidth() }, new int[]
+ {
+ (i - starty + 1) * av.charHeight + yoffset,
+ (i - starty + 1) * av.charHeight + yoffset
+ - av.charHeight / 4,
+ (i - starty + 1) * av.charHeight + 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(idfont);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param list
+ * DOCUMENT ME!
+ */
+ public void setHighlighted(List list)
+ {
+ searchResults = list;
+ repaint();
+ }
+}