X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=4c04ad37d2a409c951f2f7550ddb77a6d79496e7;hb=c6c94d2adb0d156345065b1a7e18e26c7b8dd2b8;hp=c697d1e5fe5b0eb579e3887a8c6a129d1def9c76;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index c697d1e..4c04ad3 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1,359 +1,967 @@
-package jalview.gui;
-
-import java.awt.*;
-import javax.swing.*;
-import java.util.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.analysis.*;
-
-
-public class SeqCanvas extends JPanel
-{
- Image img;
- Graphics gg;
- int imgWidth;
- int imgHeight;
-
- AlignViewport av;
- int pady = 2;
- int oldstartx;
- int oldstarty;
- int oldendx;
- int oldendy;
-
- public boolean paintFlag = false;
- boolean showScores = false;
-
- int chunkHeight;
- int chunkWidth;
-
- Graphics debugG;
- FeatureRenderer fr = new FeatureRenderer();
- BlockRenderer br = new BlockRenderer();
- CpGRenderer cgr = new CpGRenderer();
-
- ColourSchemeI cs = new ZappoColourScheme();
-
- public SeqCanvas(AlignViewport av)
- {
- this.av = av;
- setLayout(new BorderLayout());
- }
-
- public void drawScale(int startx, int endx,double charWidth, int charHeight,int ypos) {
- int scalestartx = startx - startx%10 + 10;
-
- gg.setColor(Color.black);
-
- for (int i=scalestartx;i < endx;i+= 10) {
- String string = String.valueOf(i);
- gg.drawString(string,(int)((i-startx-1)*charWidth),ypos+15 - charHeight*(2));
- }
- }
-
-
-/**
- * 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.
- */
-
- public void paintComponent(Graphics g) {
- debugG = g;
-
- AlignmentI da = av.getAlignment();
-
- if (img == null ||
- imgWidth != getWidth() ||
- imgHeight != getHeight() ||
- paintFlag == true) {
-
- imgWidth = (getWidth() > 0 ? getWidth() : 1);
- imgHeight = (getHeight() > 0 ? getHeight() : 1);
-
- img = createImage(imgWidth,imgHeight);
- gg = img.getGraphics();
-
- // SMJS I added this in to update the AV when the size changes
- // until I figure out how this should be done
- setFont(av.getFont());
-
- gg.setFont(av.getFont());
-
- paintFlag = false;
-
- oldstartx = -1;
- oldendx = -1;
- oldstarty = -1;
- oldendy = -1;
- }
-
- int startx = av.getStartRes();
- int starty = av.getStartSeq();
-
- int endx = av.getEndRes();
- int endy = av.getEndSeq();
-
- double charWidth = av.getCharWidth();
- int charHeight = av.getCharHeight();
-
- chunkWidth = (int)(getWidth()/charWidth);
- chunkHeight = (da.getHeight() + 2)*charHeight;
-
- av.setChunkHeight(chunkHeight);
- av.setChunkWidth(chunkWidth);
-
- int offy = av.getStartSeq();
-
- if (oldendx == -1) {
- fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight);
-
- /* if (av.getWrapAlignment() == true) {
- startx = (int)(offy/chunkWidth)*chunkWidth;
- endx = startx + chunkWidth;
- starty = offy%chunkHeight;
- endy = starty + da.getHeight();
-
- int ypos = 0;
- int rowstart = starty;
-
- if (starty == 0) {
- ypos = 2*charHeight;
- } else if (starty == 1) {
- starty = 0;
- ypos = charHeight;
- }
-
- if (endy > da.getHeight()) {
- endy = da.getHeight();
- }
-
- if (endx > da.getWidth()) {
- endx = da.getWidth();
- }
-
- if (rowstart < 2) {
- drawScale(startx,endx,charWidth,charHeight,ypos);
- }
-
- drawPanel(gg,startx,endx,starty,endy,startx,starty,ypos);
-
- if (rowstart == 0) {
- ypos = ypos + chunkHeight;
- } else if (rowstart == 1) {
- ypos = ypos + chunkHeight;
- } else {
- ypos = ypos + chunkHeight - rowstart*charHeight;
- }
-
- startx += chunkWidth;
- endx = startx + chunkWidth;
- starty = 0;
-
- if (endx > da.getWidth()) {
- endx = da.getWidth();
- }
- // Draw the rest of the panels
-
- while (ypos <= getHeight()) {
- drawScale(startx,endx,charWidth,charHeight,ypos);
- drawPanel(gg,startx,endx,0,da.getHeight(),startx,starty,ypos);
-
- ypos += chunkHeight;
- startx += chunkWidth;
- endx = startx + chunkWidth;
-
- if (endy > da.getHeight()) {
- endy = da.getHeight();
- }
-
- if (endx > da.getWidth()) {
- endx = da.getWidth();
- }
-
- }
- } else*/ {
- drawPanel(gg,startx,endx,starty,endy,startx,starty,0);
-
- oldstartx = startx;
- oldendx = endx;
- oldstarty = starty;
- oldendy = endy;
-
- }
- }
-
- else if (oldstartx < startx)
- {
- // This is dragging horizontal scrollbar to the right
-
- int delx = (int)((startx - oldstartx) * charWidth);
- int delx2 = (int)((oldendx - startx + 1) * charWidth);
-
- gg.copyArea(delx,0,delx2,AlignmentUtil.getPixelHeight(starty,endy,charHeight),-delx,0);
-
- if (startx > oldendx)
- drawPanel(gg,startx,endx,starty,endy,startx,starty,0);
- else
- drawPanel(gg,oldendx+1,endx,starty,endy,startx,starty,0);
-
-
- oldstartx = startx;
- oldendx = endx;
-
- } else if (oldstartx > startx)
- {
- // Horizontal scrollbar pulled to the left
-
- int delx = (int)((oldstartx - startx) * charWidth);
- int delx2 = (int)((endx - oldstartx +1) * charWidth);
-
- gg.copyArea(0,0,delx2,AlignmentUtil.getPixelHeight(starty,endy,charHeight),delx,0);
-
- if (oldstartx > endx) {
- drawPanel(gg,startx,endx,starty,endy,startx,starty,0);
- } else {
- drawPanel(gg,startx,oldstartx-1,starty,endy,startx,starty,0);
- }
-
- oldstartx = startx;
- oldendx = endx;
-
- } else if (oldstarty < starty) {
- // Vertical scrollbar down
- int dely = AlignmentUtil.getPixelHeight(oldstarty,starty,charHeight);
- int dely2 = AlignmentUtil.getPixelHeight(starty,oldendy,charHeight);
-
- gg.copyArea(0,dely,(int)((endx-startx+1)*charWidth),dely2,0,-dely);
-
- if (starty > oldendy) {
- drawPanel(gg,startx,endx,starty,endy,startx,starty,0);
- } else {
- drawPanel(gg,startx,endx,oldendy,endy,startx,starty,0);
- }
-
- oldstarty = starty;
- oldendy = endy;
-
- } else if (oldstarty > starty) {
-
- // Vertical scrollbar up
- int dely = AlignmentUtil.getPixelHeight(endy,oldendy,charHeight);
- int dely2 = AlignmentUtil.getPixelHeight(oldstarty,endy,charHeight);
-
- gg.copyArea(0,0,(int)((endx-startx+1)*charWidth),dely2,0,dely);
-
- if (oldstarty > endy) {
- drawPanel(gg,startx,endx,starty,endy,startx,starty,0);
- } else {
- drawPanel(gg,startx,endx,starty,oldstarty,startx,starty,0);
- }
-
- oldstarty = starty;
- oldendy = endy;
- }
-
- if ((oldendy -oldstarty) > (int)((getWidth() / av.getCharWidth()))) {
- System.out.println("LIMITS ERROR LIMITS ERROR");
- System.out.println("Corrds " + (oldendy-oldstarty) + " " + (int)(getWidth()/av.getCharWidth()) + " " + getWidth() + " " + av.getCharWidth());
- }
-
-
- g.drawImage(img,0,0,this);
-
- }
-
-
-
-
- public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {
-
-/*
- System.out.println("drawPanel called with g = " + g);
- System.out.println(" x1 = " + x1);
- System.out.println(" x2 = " + x2);
- System.out.println(" y1 = " + y1);
- System.out.println(" y2 = " + y2);
- System.out.println(" startx = " + startx);
- System.out.println(" starty = " + starty);
-*/
-
- g.setFont(av.getFont());
- double charWidth = av.getCharWidth();
- int charHeight = av.getCharHeight();
-
- // Vector pid = av.calcNewConsensus();
-
- RendererI sr = av.getRenderer();
-
-/* Vector tmpseq = new Vector();
-
- for (int i = 0; i < av.getAlignment().getHeight(); i++) {
- if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {
- tmpseq.addElement(av.getAlignment().getSequenceAt(i));
- }
- }
-
- if (sr instanceof SequenceRenderer) {
- pid = AAFrequency.calculate(tmpseq,x1,x2);
-
- } else if (sr instanceof GraphRenderer) {
- pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0),
- av.getAlignment().getSequences(),
- av.getPIDWindow(),x1,x2);
-
- }*/
-
- if (y2 > starty && y1 < av.getEndSeq()) {
-
- fillBackground(g,
- Color.white,
- (int)((x1-startx)*charWidth),
- offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()),
- (int)((x2-x1+1)*charWidth),
- offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight()));
- }
-
- for (int i = y1 ; i < y2 ;i++) {
-
- RendererI r = sr;
-
- /* if (av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {
- r = fr;
- System.out.println("use feature renderer");
- // } else if ( i == 0) {
- // r = br;
- } else if (av.getAlignment().getSequenceAt(i).getName().equals("CpG")) {
- r = cgr;
- System.out.println("cg renderer");
- }*/
-
- r.drawSequence(g,cs,av.getAlignment().getSequenceAt(i),
- x1,
- x2,
- (int)((x1-startx)*charWidth),
- offset + AlignmentUtil.getPixelHeight(starty,i,av.getCharHeight()),
- charWidth,
- charHeight,showScores,av.getShowBoxes(),av.getShowText(),null,i,av);
-
- }
- }
-
-
-
- public void fillBackground(Graphics g,Color c, int x1,int y1,int width,int height) {
- g.setColor(c);
- g.fillRect(x1,y1,width,height);
- }
-
- public int getChunkWidth() {
- return chunkWidth;
- }
-
-}
+/*
+ * 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 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();
+ int scalestartx = startx - (startx % 10) + 10;
+
+ g.setColor(Color.black);
+ // NORTH SCALE
+ for (int i = scalestartx; i < endx; i += 10)
+ {
+ int value = i;
+ if (av.hasHiddenColumns())
+ {
+ value = av.getColumnSelection().adjustForHiddenColumns(value);
+ }
+
+ g.drawString(String.valueOf(value), (i - startx - 1) * charWidth,
+ ypos - (charHeight / 2));
+
+ g.drawLine(((i - startx - 1) * charWidth) + (charWidth / 2),
+ (ypos + 2) - (charHeight / 2), ((i - startx - 1) * 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
+ 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))
+ {
+ 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();
+ }
+}