X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=760ece0c6d00f11454d66f77c4ffc8309d5b0c94;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=afb5a36e6262d79963dccdececf5749d8a214e0c;hpb=a6359c6eb746b06030b22135ed20417b971f580f;p=jalview.git
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index afb5a36..760ece0 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1,673 +1,976 @@
-/*
- * 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 SeqCanvas extends JComponent
-{
- FeatureRenderer fr;
- SequenceRenderer sr;
- BufferedImage img;
- Graphics2D gg;
- int imgWidth;
- int imgHeight;
- AlignViewport av;
- boolean displaySearch = false;
- int[] searchResults = null;
- int chunkHeight;
- int chunkWidth;
- boolean fastPaint = false;
- int LABEL_WEST;
- int LABEL_EAST;
-
- /**
- * Creates a new SeqCanvas object.
- *
- * @param av DOCUMENT ME!
- */
- public SeqCanvas(AlignViewport av)
- {
- this.av = av;
- fr = new FeatureRenderer(av);
- sr = new SequenceRenderer(av);
- setLayout(new BorderLayout());
- PaintRefresher.Register(this, av.alignment);
- setBackground(Color.white);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param startx DOCUMENT ME!
- * @param endx DOCUMENT ME!
- * @param ypos DOCUMENT ME!
- */
- void drawNorthScale(Graphics g, int startx, int endx, int ypos)
- {
- int scalestartx = startx - (startx % 10) + 10;
-
- g.setColor(Color.black);
-
- // NORTH SCALE
- for (int i = scalestartx; i < endx; i += 10)
- {
- String string = String.valueOf(i);
- g.drawString(string, (i - startx - 1) * av.charWidth,
- ypos - (av.charHeight / 2));
-
- g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
- (ypos + 2) - (av.charHeight / 2),
- ((i - startx - 1) * av.charWidth) + (av.charWidth / 2), ypos -
- 2);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param startx DOCUMENT ME!
- * @param endx DOCUMENT ME!
- * @param ypos DOCUMENT ME!
- */
- void drawWestScale(Graphics g, int startx, int endx, int ypos)
- {
- FontMetrics fm = getFontMetrics(av.getFont());
- ypos += av.charHeight;
-
- // EAST SCALE
- for (int i = 0; i < av.alignment.getHeight(); i++)
- {
- SequenceI seq = av.alignment.getSequenceAt(i);
- int index = startx;
- int value = -1;
-
- while (index < endx)
- {
- if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
- {
- index++;
-
- continue;
- }
-
- value = av.alignment.getSequenceAt(i).findPosition(index);
-
- break;
- }
-
- if (value != -1)
- {
- int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))-av.charWidth/2;
- g.drawString(value + "", x,
- (ypos + (i * av.charHeight)) - (av.charHeight / 5));
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param startx DOCUMENT ME!
- * @param endx DOCUMENT ME!
- * @param ypos DOCUMENT ME!
- */
- void drawEastScale(Graphics g, int startx, int endx, int ypos)
- {
- ypos += av.charHeight;
-
- // EAST SCALE
- for (int i = 0; i < av.alignment.getHeight(); i++)
- {
- SequenceI seq = av.alignment.getSequenceAt(i);
- int index = endx;
- int value = -1;
-
- while (index > startx)
- {
- if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
- {
- index--;
-
- continue;
- }
-
- value = av.alignment.getSequenceAt(i).findPosition(index);
-
- break;
- }
-
- if (value != -1)
- {
- g.drawString(String.valueOf(value), av.charWidth/2,
- (ypos + (i * av.charHeight)) - (av.charHeight / 5));
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param horizontal DOCUMENT ME!
- * @param vertical DOCUMENT ME!
- */
- public void fastPaint(int horizontal, int vertical)
- {
- if (((horizontal == 0) && (vertical == 0)) || (gg == null))
- {
- return;
- }
-
- gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,
- -vertical * av.charHeight);
-
- int sr = av.startRes;
- int er = av.endRes;
- int ss = av.startSeq;
- int es = av.endSeq;
- int transX = 0;
- int transY = 0;
-
- if (horizontal > 0) // scrollbar pulled right, image to the left
- {
- transX = (er - sr - horizontal) * av.charWidth;
- sr = er - horizontal;
- }
- else if (horizontal < 0)
- {
- er = sr - horizontal;
- }
- else 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(transX, transY);
-
- gg.setColor(Color.white);
- gg.fillRect(0, 0, (er - sr + 1) * av.charWidth,
- (es - ss) * av.charHeight);
- drawPanel(gg, sr, er, ss, es, sr, ss, 0);
- gg.translate(-transX, -transY);
-
- fastPaint = true;
- repaint();
- }
-
- /**
- * Definitions of startx and endx (hopefully):
- * SMJS This is what I'm working towards!
- * startx is the first residue (starting at 0) to display.
- * endx is the last residue to display (starting at 0).
- * starty is the first sequence to display (starting at 0).
- * endy is the last sequence to display (starting at 0).
- * NOTE 1: The av limits are set in setFont in this class and
- * in the adjustment listener in SeqPanel when the scrollbars move.
- */
-
- // Set this to false to force a full panel paint
- public void paintComponent(Graphics g)
- {
- if ((img != null) &&
- (fastPaint || (getWidth() != g.getClipBounds().width) ||
- (getHeight() != g.getClipBounds().height)))
- {
- g.drawImage(img, 0, 0, this);
- fastPaint = false;
-
- return;
- }
-
- // this draws the whole of the alignment
- imgWidth = getWidth();
- imgHeight = getHeight();
-
- imgWidth -= (imgWidth % av.charWidth);
- imgHeight -= (imgHeight % av.charHeight);
-
- if ((imgWidth < 1) || (imgHeight < 1))
- {
- return;
- }
-
- img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);
- gg = (Graphics2D) img.getGraphics();
- gg.setFont(av.getFont());
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
-
- gg.setColor(Color.white);
- gg.fillRect(0, 0, imgWidth, imgHeight);
-
- chunkWidth = getWrappedCanvasWidth(getWidth());
- chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
-
- av.setChunkHeight(chunkHeight);
- av.setChunkWidth(chunkWidth);
-
- if (av.getWrapAlignment())
- {
- drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
- }
- else
- {
- drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq,
- av.startRes, av.startSeq, 0);
- }
-
- g.drawImage(img, 0, 0, this);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param cwidth DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getWrappedCanvasWidth(int cwidth)
- {
- FontMetrics fm = getFontMetrics(av.getFont());
-
- LABEL_EAST = 0;
- LABEL_WEST = 0;
-
- if (av.scaleRightWrapped)
- {
- LABEL_EAST = fm.stringWidth(getMask()+"0");
- }
-
- if (av.scaleLeftWrapped)
- {
- LABEL_WEST = fm.stringWidth(getMask());
- }
-
- return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
- }
-
-
- /**
- * Generates a string of zeroes.
- * @return String
- */
- String getMask()
- {
- String mask = "0";
- for (int i = av.alignment.getWidth(); i > 0; i /= 10)
- {
- mask += "0";
- }
- return mask;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param canvasWidth DOCUMENT ME!
- * @param canvasHeight DOCUMENT ME!
- * @param startRes DOCUMENT ME!
- */
- public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
- int startRes)
- {
-
- AlignmentI al = av.getAlignment();
-
- FontMetrics fm = getFontMetrics(av.getFont());
-
- int LABEL_EAST = 0;
-
- if (av.scaleRightWrapped)
- {
- LABEL_EAST = fm.stringWidth(getMask()+"0");
- }
-
- int LABEL_WEST = 0;
-
- if (av.scaleLeftWrapped)
- {
- LABEL_WEST = fm.stringWidth(getMask());
- }
-
- int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
- int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
-
- av.endRes = av.startRes + cWidth;
-
- int endx = (startRes + cWidth) - 1;
- int ypos = 2 * av.charHeight;
-
- while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
- {
- g.setColor(Color.black);
-
- if (av.scaleLeftWrapped)
- {
- drawWestScale(g, startRes, endx, ypos);
- }
-
- if (av.scaleRightWrapped)
- {
- g.translate(canvasWidth - LABEL_EAST, 0);
- drawEastScale(g, startRes, endx, ypos);
- g.translate(-(canvasWidth - LABEL_EAST), 0);
- }
-
- g.translate(LABEL_WEST, 0);
-
- if (av.scaleAboveWrapped)
- {
- drawNorthScale(g, startRes, endx, ypos);
- }
-
- // When printing we have an extra clipped region,
- // the Printable page which we need to account for here
- Shape clip = g.getClip();
-
- if (clip == null)
- {
- g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
- }
- else
- {
- g.setClip(0, (int) clip.getBounds().getY(),
- cWidth * av.charWidth, (int) clip.getBounds().getHeight());
- }
-
- drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
- g.setClip(clip);
- g.translate(-LABEL_WEST, 0);
-
- ypos += cHeight;
- startRes += cWidth;
- endx = (startRes + cWidth) - 1;
-
- if (endx > al.getWidth())
- {
- endx = al.getWidth();
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g1 DOCUMENT ME!
- * @param x1 DOCUMENT ME!
- * @param x2 DOCUMENT ME!
- * @param y1 DOCUMENT ME!
- * @param y2 DOCUMENT ME!
- * @param startx DOCUMENT ME!
- * @param starty DOCUMENT ME!
- * @param offset DOCUMENT ME!
- */
- synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,
- int y2, int startx, int starty, int offset)
- {
- Graphics2D g = (Graphics2D) g1;
- g.setFont(av.getFont());
- sr.renderGaps(av.renderGaps);
-
- SequenceI nextSeq;
-
- /// First draw the sequences
- /////////////////////////////
- for (int i = y1; i < y2; i++)
- {
- nextSeq = av.alignment.getSequenceAt(i);
-
- sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),
- x1, x2, (x1 - startx) * av.charWidth,
- offset + ((i - starty) * av.charHeight), av.charWidth,
- av.charHeight);
-
- if (av.showSequenceFeatures)
- {
- fr.drawSequence(g, nextSeq,
- av.alignment.findAllGroups(nextSeq), x1, x2,
- (x1 - startx) * av.charWidth,
- offset + ((i - starty) * av.charHeight), av.charWidth,
- av.charHeight);
- }
- }
-
- //
- /////////////////////////////////////
- // Now outline any areas if necessary
- /////////////////////////////////////
- SequenceGroup group = av.getSelectionGroup();
- java.util.Vector groups = av.alignment.getGroups();
-
- int sx = -1;
- int sy = -1;
- int ex = -1;
- int groupIndex = -1;
-
- if ((group == null) && (groups.size() > 0))
- {
- group = (SequenceGroup) groups.elementAt(0);
- groupIndex = 0;
- }
-
-
- if (group != null)
- {
- do
- {
- int oldY = -1;
- int i = 0;
- boolean inGroup = false;
- int top = -1;
- int bottom = -1;
-
- for (i = y1; i < y2; i++)
- {
- sx = (group.getStartRes() - startx) * av.charWidth;
- sy = offset + ((i - starty) * av.charHeight);
- ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -
- 1;
-
-
- if ((sx < (x2-x1)*av.charWidth) &&
- group.sequences.contains(av.alignment.getSequenceAt(
- i)))
- {
- if ((bottom == -1) &&
- !group.sequences.contains(
- av.alignment.getSequenceAt(i + 1)))
- {
- bottom = sy + av.charHeight;
- }
-
- if (!inGroup)
- {
- if (((top == -1) && (i == 0)) ||
- !group.sequences.contains(
- av.alignment.getSequenceAt(i - 1)))
- {
- top = sy;
- }
-
- oldY = sy;
- inGroup = true;
-
- if (group == av.getSelectionGroup())
- {
- g.setStroke(new BasicStroke(1,
- BasicStroke.CAP_BUTT,
- BasicStroke.JOIN_ROUND, 3f,
- new float[] { 5f, 3f }, 0f));
- g.setColor(Color.RED);
- }
- else
- {
- g.setStroke(new BasicStroke());
- g.setColor(group.getOutlineColour());
- }
- }
- }
- else
- {
- if (inGroup)
- {
- g.drawLine(sx, oldY, sx, sy);
- g.drawLine(sx + ex, oldY, sx + ex, sy);
-
- if (top != -1)
- {
- g.drawLine(sx, top, sx + ex, top);
- top = -1;
- }
-
- if (bottom != -1)
- {
- g.drawLine(sx, bottom, sx + ex, bottom);
- bottom = -1;
- }
-
- inGroup = false;
- }
- }
- }
-
-
- if (inGroup)
- {
- if (top != -1)
- {
- g.drawLine(sx, top, sx + ex, top);
- top = -1;
- }
-
- if (bottom != -1)
- {
- g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
- bottom = -1;
- }
-
- sy = offset + ((i - starty) * av.charHeight);
- g.drawLine(sx, oldY, sx, sy);
- g.drawLine(sx + ex, oldY, sx + ex, sy);
- inGroup = false;
- }
-
- groupIndex++;
-
- if (groupIndex >= groups.size())
- {
- break;
- }
-
- group = (SequenceGroup) groups.elementAt(groupIndex);
- }
- while (groupIndex < groups.size());
- }
-
- /// Highlight search Results once all sequences have been drawn
- //////////////////////////////////////////////////////////
- if (displaySearch)
- {
- for (int r = 0; r < searchResults.length; r += 3)
- {
- int searchSeq = searchResults[r];
-
- if ((searchSeq >= y1) && (searchSeq < y2))
- {
- SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);
-
- int searchStart = seq.findIndex(searchResults[r + 1]) - 1;
- int searchEnd = seq.findIndex(searchResults[r + 2]) - 1;
-
- SequenceRenderer ssr = (SequenceRenderer) sr;
-
- if (searchStart < x1)
- {
- searchStart = x1;
- }
-
- if (searchEnd > x2)
- {
- searchEnd = x2;
- }
-
- ssr.drawHighlightedText(seq, searchStart, searchEnd,
- (searchStart - startx) * av.charWidth,
- offset + ((searchSeq - starty) * av.charHeight),
- av.charWidth, av.charHeight);
- }
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param results DOCUMENT ME!
- */
- public void highlightSearchResults(int[] results)
- {
- // results are in the order sequence, startRes, endRes
- if (results == null)
- {
- displaySearch = false;
- }
- else
- {
- displaySearch = true;
- }
-
- searchResults = results;
-
- repaint();
- }
-}
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.ScaleRenderer;
+import jalview.renderer.ScaleRenderer.ScaleMark;
+
+import java.awt.BasicStroke;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.Shape;
+import java.awt.image.BufferedImage;
+import java.util.List;
+
+import javax.swing.JComponent;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SeqCanvas extends JComponent
+{
+ final FeatureRenderer fr;
+
+ final SequenceRenderer sr;
+
+ BufferedImage img;
+
+ Graphics2D gg;
+
+ int imgWidth;
+
+ int imgHeight;
+
+ AlignViewport av;
+
+ SearchResults searchResults = null;
+
+ boolean fastPaint = false;
+
+ int LABEL_WEST;
+
+ int LABEL_EAST;
+
+ int cursorX = 0;
+
+ int cursorY = 0;
+
+ /**
+ * Creates a new SeqCanvas object.
+ *
+ * @param av
+ * DOCUMENT ME!
+ */
+ public SeqCanvas(AlignmentPanel ap)
+ {
+ this.av = ap.av;
+ updateViewport();
+ fr = new FeatureRenderer(ap);
+ sr = new SequenceRenderer(av);
+ setLayout(new BorderLayout());
+ PaintRefresher.Register(this, av.getSequenceSetId());
+ setBackground(Color.white);
+ }
+
+ public SequenceRenderer getSequenceRenderer()
+ {
+ return sr;
+ }
+
+ public FeatureRenderer getFeatureRenderer()
+ {
+ return fr;
+ }
+
+ int charHeight = 0, charWidth = 0;
+
+ private void updateViewport()
+ {
+ charHeight = av.getCharHeight();
+ charWidth = av.getCharWidth();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startx
+ * DOCUMENT ME!
+ * @param endx
+ * DOCUMENT ME!
+ * @param ypos
+ * DOCUMENT ME!
+ */
+ private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
+ {
+ updateViewport();
+ for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx,
+ endx))
+ {
+ int mpos = mark.column; // (i - startx - 1)
+ if (mpos < 0)
+ {
+ continue;
+ }
+ String mstring = mark.text;
+
+ if (mark.major)
+ {
+ if (mstring != null)
+ {
+ g.drawString(mstring, mpos * charWidth, ypos - (charHeight / 2));
+ }
+ g.drawLine((mpos * charWidth) + (charWidth / 2), (ypos + 2)
+ - (charHeight / 2), (mpos * charWidth) + (charWidth / 2),
+ ypos - 2);
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startx
+ * DOCUMENT ME!
+ * @param endx
+ * DOCUMENT ME!
+ * @param ypos
+ * DOCUMENT ME!
+ */
+ void drawWestScale(Graphics g, int startx, int endx, int ypos)
+ {
+ FontMetrics fm = getFontMetrics(av.getFont());
+ ypos += charHeight;
+
+ if (av.hasHiddenColumns())
+ {
+ startx = av.getColumnSelection().adjustForHiddenColumns(startx);
+ endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+ }
+
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ }
+
+ // WEST SCALE
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
+ {
+ SequenceI seq = av.getAlignment().getSequenceAt(i);
+ int index = startx;
+ int value = -1;
+
+ while (index < endx)
+ {
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+ {
+ index++;
+
+ continue;
+ }
+
+ value = av.getAlignment().getSequenceAt(i).findPosition(index);
+
+ break;
+ }
+
+ if (value != -1)
+ {
+ int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
+ - charWidth / 2;
+ g.drawString(value + "", x, (ypos + (i * charHeight))
+ - (charHeight / 5));
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startx
+ * DOCUMENT ME!
+ * @param endx
+ * DOCUMENT ME!
+ * @param ypos
+ * DOCUMENT ME!
+ */
+ void drawEastScale(Graphics g, int startx, int endx, int ypos)
+ {
+ ypos += charHeight;
+
+ if (av.hasHiddenColumns())
+ {
+ endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+ }
+
+ SequenceI seq;
+ // EAST SCALE
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
+ {
+ seq = av.getAlignment().getSequenceAt(i);
+ int index = endx;
+ int value = -1;
+
+ while (index > startx)
+ {
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+ {
+ index--;
+
+ continue;
+ }
+
+ value = seq.findPosition(index);
+
+ break;
+ }
+
+ if (value != -1)
+ {
+ g.drawString(String.valueOf(value), 0, (ypos + (i * charHeight))
+ - (charHeight / 5));
+ }
+ }
+ }
+
+ boolean fastpainting = false;
+
+ /**
+ * need to make this thread safe move alignment rendering in response to
+ * slider adjustment
+ *
+ * @param horizontal
+ * shift along
+ * @param vertical
+ * shift up or down in repaint
+ */
+ public void fastPaint(int horizontal, int vertical)
+ {
+ if (fastpainting || gg == null)
+ {
+ return;
+ }
+ fastpainting = true;
+ fastPaint = true;
+ updateViewport();
+ gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
+ imgHeight, -horizontal * charWidth, -vertical * charHeight);
+
+ int sr = av.startRes;
+ int er = av.endRes;
+ int ss = av.startSeq;
+ int es = av.endSeq;
+ int transX = 0;
+ int transY = 0;
+
+ if (horizontal > 0) // scrollbar pulled right, image to the left
+ {
+ er++;
+ transX = (er - sr - horizontal) * charWidth;
+ sr = er - horizontal;
+ }
+ else if (horizontal < 0)
+ {
+ er = sr - horizontal - 1;
+ }
+ else 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 * charHeight);
+ }
+ }
+ else if (vertical < 0)
+ {
+ es = ss - vertical;
+
+ if (es > av.endSeq)
+ {
+ es = av.endSeq;
+ }
+ }
+
+ gg.translate(transX, transY);
+ drawPanel(gg, sr, er, ss, es, 0);
+ gg.translate(-transX, -transY);
+
+ repaint();
+ fastpainting = false;
+ }
+
+ /**
+ * Definitions of startx and endx (hopefully): SMJS This is what I'm working
+ * towards! startx is the first residue (starting at 0) to display. endx is
+ * the last residue to display (starting at 0). starty is the first sequence
+ * to display (starting at 0). endy is the last sequence to display (starting
+ * at 0). NOTE 1: The av limits are set in setFont in this class and in the
+ * adjustment listener in SeqPanel when the scrollbars move.
+ */
+
+ // Set this to false to force a full panel paint
+ @Override
+ public void paintComponent(Graphics g)
+ {
+ updateViewport();
+ BufferedImage lcimg = img; // take reference since other threads may null
+ // img and call later.
+ super.paintComponent(g);
+
+ if (lcimg != null
+ && (fastPaint
+ || (getVisibleRect().width != g.getClipBounds().width) || (getVisibleRect().height != g
+ .getClipBounds().height)))
+ {
+ g.drawImage(lcimg, 0, 0, this);
+ fastPaint = false;
+ return;
+ }
+
+ // this draws the whole of the alignment
+ imgWidth = getWidth();
+ imgHeight = getHeight();
+
+ imgWidth -= (imgWidth % charWidth);
+ imgHeight -= (imgHeight % charHeight);
+
+ if ((imgWidth < 1) || (imgHeight < 1))
+ {
+ return;
+ }
+
+ if (lcimg == null || imgWidth != lcimg.getWidth()
+ || imgHeight != lcimg.getHeight())
+ {
+ try
+ {
+ lcimg = img = new BufferedImage(imgWidth, imgHeight,
+ BufferedImage.TYPE_INT_RGB);
+ gg = (Graphics2D) img.getGraphics();
+ gg.setFont(av.getFont());
+ } catch (OutOfMemoryError er)
+ {
+ System.gc();
+ System.err.println("SeqCanvas OutOfMemory Redraw Error.\n" + er);
+ new OOMWarning("Creating alignment image for display", er);
+
+ return;
+ }
+ }
+
+ if (av.antiAlias)
+ {
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ }
+
+ gg.setColor(Color.white);
+ gg.fillRect(0, 0, imgWidth, imgHeight);
+
+ if (av.getWrapAlignment())
+ {
+ drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
+ }
+ else
+ {
+ drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+ }
+
+ g.drawImage(lcimg, 0, 0, this);
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cwidth
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getWrappedCanvasWidth(int cwidth)
+ {
+ FontMetrics fm = getFontMetrics(av.getFont());
+
+ LABEL_EAST = 0;
+ LABEL_WEST = 0;
+
+ if (av.getScaleRightWrapped())
+ {
+ LABEL_EAST = fm.stringWidth(getMask());
+ }
+
+ if (av.getScaleLeftWrapped())
+ {
+ LABEL_WEST = fm.stringWidth(getMask());
+ }
+
+ return (cwidth - LABEL_EAST - LABEL_WEST) / charWidth;
+ }
+
+ /**
+ * Generates a string of zeroes.
+ *
+ * @return String
+ */
+ String getMask()
+ {
+ String mask = "00";
+ int maxWidth = 0;
+ int tmp;
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
+ {
+ tmp = av.getAlignment().getSequenceAt(i).getEnd();
+ if (tmp > maxWidth)
+ {
+ maxWidth = tmp;
+ }
+ }
+
+ for (int i = maxWidth; i > 0; i /= 10)
+ {
+ mask += "0";
+ }
+ return mask;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param canvasWidth
+ * DOCUMENT ME!
+ * @param canvasHeight
+ * DOCUMENT ME!
+ * @param startRes
+ * DOCUMENT ME!
+ */
+ public void drawWrappedPanel(Graphics g, int canvasWidth,
+ int canvasHeight, int startRes)
+ {
+ updateViewport();
+ AlignmentI al = av.getAlignment();
+
+ FontMetrics fm = getFontMetrics(av.getFont());
+
+ if (av.getScaleRightWrapped())
+ {
+ LABEL_EAST = fm.stringWidth(getMask());
+ }
+
+ if (av.getScaleLeftWrapped())
+ {
+ LABEL_WEST = fm.stringWidth(getMask());
+ }
+
+ int hgap = charHeight;
+ if (av.getScaleAboveWrapped())
+ {
+ hgap += charHeight;
+ }
+
+ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / charWidth;
+ int cHeight = av.getAlignment().getHeight() * charHeight;
+
+ av.setWrappedWidth(cWidth);
+
+ av.endRes = av.startRes + cWidth;
+
+ int endx;
+ int ypos = hgap;
+ int maxwidth = av.getAlignment().getWidth() - 1;
+
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ }
+
+ while ((ypos <= canvasHeight) && (startRes < maxwidth))
+ {
+ endx = startRes + cWidth - 1;
+
+ if (endx > maxwidth)
+ {
+ endx = maxwidth;
+ }
+
+ g.setFont(av.getFont());
+ g.setColor(Color.black);
+
+ if (av.getScaleLeftWrapped())
+ {
+ drawWestScale(g, startRes, endx, ypos);
+ }
+
+ if (av.getScaleRightWrapped())
+ {
+ g.translate(canvasWidth - LABEL_EAST, 0);
+ drawEastScale(g, startRes, endx, ypos);
+ g.translate(-(canvasWidth - LABEL_EAST), 0);
+ }
+
+ g.translate(LABEL_WEST, 0);
+
+ if (av.getScaleAboveWrapped())
+ {
+ drawNorthScale(g, startRes, endx, ypos);
+ }
+
+ if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
+ {
+ g.setColor(Color.blue);
+ int res;
+ for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
+ .size(); i++)
+ {
+ res = av.getColumnSelection().findHiddenRegionPosition(i)
+ - startRes;
+
+ if (res < 0 || res > endx - startRes)
+ {
+ continue;
+ }
+
+ gg.fillPolygon(
+ new int[] { res * charWidth - charHeight / 4,
+ res * charWidth + charHeight / 4, res * charWidth },
+ new int[] { ypos - (charHeight / 2),
+ ypos - (charHeight / 2), ypos - (charHeight / 2) + 8 },
+ 3);
+
+ }
+ }
+
+ // When printing we have an extra clipped region,
+ // the Printable page which we need to account for here
+ Shape clip = g.getClip();
+
+ if (clip == null)
+ {
+ g.setClip(0, 0, cWidth * charWidth, canvasHeight);
+ }
+ else
+ {
+ g.setClip(0, (int) clip.getBounds().getY(), cWidth * charWidth,
+ (int) clip.getBounds().getHeight());
+ }
+
+ drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+
+ if (av.isShowAnnotation())
+ {
+ g.translate(0, cHeight + ypos + 3);
+ if (annotations == null)
+ {
+ annotations = new AnnotationPanel(av);
+ }
+
+ annotations.renderer.drawComponent(annotations, av, g, -1,
+ startRes, endx + 1);
+ g.translate(0, -cHeight - ypos - 3);
+ }
+ g.setClip(clip);
+ g.translate(-LABEL_WEST, 0);
+
+ ypos += cHeight + getAnnotationHeight() + hgap;
+
+ startRes += cWidth;
+ }
+ }
+
+ AnnotationPanel annotations;
+
+ int getAnnotationHeight()
+ {
+ if (!av.isShowAnnotation())
+ {
+ return 0;
+ }
+
+ if (annotations == null)
+ {
+ annotations = new AnnotationPanel(av);
+ }
+
+ return annotations.adjustPanelHeight();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g1
+ * DOCUMENT ME!
+ * @param startRes
+ * DOCUMENT ME!
+ * @param endRes
+ * DOCUMENT ME!
+ * @param startSeq
+ * DOCUMENT ME!
+ * @param endSeq
+ * DOCUMENT ME!
+ * @param offset
+ * DOCUMENT ME!
+ */
+ public void drawPanel(Graphics g1, int startRes, int endRes,
+ int startSeq, int endSeq, int offset)
+ {
+ updateViewport();
+ if (!av.hasHiddenColumns())
+ {
+ draw(g1, startRes, endRes, startSeq, endSeq, offset);
+ }
+ else
+ {
+ List regions = av.getColumnSelection().getHiddenColumns();
+
+ int screenY = 0;
+ int blockStart = startRes;
+ int blockEnd = endRes;
+
+ for (int[] region : regions)
+ {
+ int hideStart = region[0];
+ int hideEnd = region[1];
+
+ if (hideStart <= blockStart)
+ {
+ blockStart += (hideEnd - hideStart) + 1;
+ continue;
+ }
+
+ blockEnd = hideStart - 1;
+
+ g1.translate(screenY * charWidth, 0);
+
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+
+ if (av.getShowHiddenMarkers())
+ {
+ g1.setColor(Color.blue);
+
+ g1.drawLine((blockEnd - blockStart + 1) * charWidth - 1,
+ 0 + offset, (blockEnd - blockStart + 1) * charWidth - 1,
+ (endSeq - startSeq) * charHeight + offset);
+ }
+
+ g1.translate(-screenY * charWidth, 0);
+ screenY += blockEnd - blockStart + 1;
+ blockStart = hideEnd + 1;
+
+ if (screenY > (endRes - startRes))
+ {
+ // already rendered last block
+ return;
+ }
+ }
+
+ if (screenY <= (endRes - startRes))
+ {
+ // remaining visible region to render
+ blockEnd = blockStart + (endRes - startRes) - screenY;
+ g1.translate(screenY * charWidth, 0);
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+
+ g1.translate(-screenY * charWidth, 0);
+ }
+ }
+
+ }
+
+ // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
+ // int x1, int x2, int y1, int y2, int startx, int starty,
+ private void draw(Graphics g, int startRes, int endRes, int startSeq,
+ int endSeq, int offset)
+ {
+ g.setFont(av.getFont());
+ sr.prepare(g, av.isRenderGaps());
+
+ SequenceI nextSeq;
+
+ // / First draw the sequences
+ // ///////////////////////////
+ for (int i = startSeq; i < endSeq; i++)
+ {
+ nextSeq = av.getAlignment().getSequenceAt(i);
+ if (nextSeq == null)
+ {
+ // occasionally, a race condition occurs such that the alignment row is
+ // empty
+ continue;
+ }
+ sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
+ startRes, endRes, offset + ((i - startSeq) * charHeight));
+
+ if (av.isShowSequenceFeatures())
+ {
+ fr.drawSequence(g, nextSeq, startRes, endRes, offset
+ + ((i - startSeq) * charHeight));
+ }
+
+ // / Highlight search Results once all sequences have been drawn
+ // ////////////////////////////////////////////////////////
+ if (searchResults != null)
+ {
+ int[] visibleResults = searchResults.getResults(nextSeq, startRes,
+ endRes);
+ if (visibleResults != null)
+ {
+ for (int r = 0; r < visibleResults.length; r += 2)
+ {
+ sr.drawHighlightedText(nextSeq, visibleResults[r],
+ visibleResults[r + 1], (visibleResults[r] - startRes)
+ * charWidth, offset
+ + ((i - startSeq) * charHeight));
+ }
+ }
+ }
+
+ if (av.cursorMode && cursorY == i && cursorX >= startRes
+ && cursorX <= endRes)
+ {
+ sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth,
+ offset + ((i - startSeq) * charHeight));
+ }
+ }
+
+ if (av.getSelectionGroup() != null
+ || av.getAlignment().getGroups().size() > 0)
+ {
+ drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
+ }
+
+ }
+
+ void drawGroupsBoundaries(Graphics g1, int startRes, int endRes,
+ int startSeq, int endSeq, int offset)
+ {
+ Graphics2D g = (Graphics2D) g1;
+ //
+ // ///////////////////////////////////
+ // Now outline any areas if necessary
+ // ///////////////////////////////////
+ SequenceGroup group = av.getSelectionGroup();
+
+ int sx = -1;
+ int sy = -1;
+ int ex = -1;
+ int groupIndex = -1;
+ int visWidth = (endRes - startRes + 1) * charWidth;
+
+ if ((group == null) && (av.getAlignment().getGroups().size() > 0))
+ {
+ group = av.getAlignment().getGroups().get(0);
+ groupIndex = 0;
+ }
+
+ if (group != null)
+ {
+ do
+ {
+ int oldY = -1;
+ int i = 0;
+ boolean inGroup = false;
+ int top = -1;
+ int bottom = -1;
+
+ for (i = startSeq; i < endSeq; i++)
+ {
+ sx = (group.getStartRes() - startRes) * charWidth;
+ sy = offset + ((i - startSeq) * charHeight);
+ ex = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth) - 1;
+
+ if (sx + ex < 0 || sx > visWidth)
+ {
+ continue;
+ }
+
+ if ((sx <= (endRes - startRes) * charWidth)
+ && group.getSequences(null).contains(
+ av.getAlignment().getSequenceAt(i)))
+ {
+ if ((bottom == -1)
+ && !group.getSequences(null).contains(
+ av.getAlignment().getSequenceAt(i + 1)))
+ {
+ bottom = sy + charHeight;
+ }
+
+ if (!inGroup)
+ {
+ if (((top == -1) && (i == 0))
+ || !group.getSequences(null).contains(
+ av.getAlignment().getSequenceAt(i - 1)))
+ {
+ top = sy;
+ }
+
+ oldY = sy;
+ inGroup = true;
+
+ if (group == av.getSelectionGroup())
+ {
+ g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
+ BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f },
+ 0f));
+ g.setColor(Color.RED);
+ }
+ else
+ {
+ g.setStroke(new BasicStroke());
+ g.setColor(group.getOutlineColour());
+ }
+ }
+ }
+ else
+ {
+ if (inGroup)
+ {
+ if (sx >= 0 && sx < visWidth)
+ {
+ g.drawLine(sx, oldY, sx, sy);
+ }
+
+ if (sx + ex < visWidth)
+ {
+ g.drawLine(sx + ex, oldY, sx + ex, sy);
+ }
+
+ if (sx < 0)
+ {
+ ex += sx;
+ sx = 0;
+ }
+
+ if (sx + ex > visWidth)
+ {
+ ex = visWidth;
+ }
+
+ else if (sx + ex >= (endRes - startRes + 1) * charWidth)
+ {
+ ex = (endRes - startRes + 1) * charWidth;
+ }
+
+ if (top != -1)
+ {
+ g.drawLine(sx, top, sx + ex, top);
+ top = -1;
+ }
+
+ if (bottom != -1)
+ {
+ g.drawLine(sx, bottom, sx + ex, bottom);
+ bottom = -1;
+ }
+
+ inGroup = false;
+ }
+ }
+ }
+
+ if (inGroup)
+ {
+ sy = offset + ((i - startSeq) * charHeight);
+ if (sx >= 0 && sx < visWidth)
+ {
+ g.drawLine(sx, oldY, sx, sy);
+ }
+
+ if (sx + ex < visWidth)
+ {
+ g.drawLine(sx + ex, oldY, sx + ex, sy);
+ }
+
+ if (sx < 0)
+ {
+ ex += sx;
+ sx = 0;
+ }
+
+ if (sx + ex > visWidth)
+ {
+ ex = visWidth;
+ }
+ else if (sx + ex >= (endRes - startRes + 1) * charWidth)
+ {
+ ex = (endRes - startRes + 1) * charWidth;
+ }
+
+ if (top != -1)
+ {
+ g.drawLine(sx, top, sx + ex, top);
+ top = -1;
+ }
+
+ if (bottom != -1)
+ {
+ g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
+ bottom = -1;
+ }
+
+ inGroup = false;
+ }
+
+ groupIndex++;
+
+ g.setStroke(new BasicStroke());
+
+ if (groupIndex >= av.getAlignment().getGroups().size())
+ {
+ break;
+ }
+
+ group = av.getAlignment().getGroups().get(groupIndex);
+
+ } while (groupIndex < av.getAlignment().getGroups().size());
+
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param results
+ * DOCUMENT ME!
+ */
+ public void highlightSearchResults(SearchResults results)
+ {
+ img = null;
+
+ searchResults = results;
+
+ repaint();
+ }
+}