+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
+import jalview.datamodel.*;\r
+\r
import java.awt.*;\r
+import java.awt.image.*;\r
+\r
import javax.swing.*;\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
+import jalview.schemes.*;\r
\r
\r
-public class SeqCanvas extends JPanel\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class SeqCanvas extends JComponent\r
{\r
- FeatureRenderer fr;\r
- Image img;\r
- Graphics2D gg;\r
- int imgWidth;\r
- int imgHeight;\r
+ FeatureRenderer fr;\r
+ SequenceRenderer sr;\r
+ BufferedImage img;\r
+ Graphics2D gg;\r
+ int imgWidth;\r
+ int imgHeight;\r
+ AlignViewport av;\r
+ boolean displaySearch = false;\r
+ int[] searchResults = null;\r
+ boolean fastPaint = false;\r
+ int LABEL_WEST;\r
+ int LABEL_EAST;\r
+\r
+ /**\r
+ * Creates a new SeqCanvas object.\r
+ *\r
+ * @param av DOCUMENT ME!\r
+ */\r
+ public SeqCanvas(AlignViewport av)\r
+ {\r
+ this.av = av;\r
+ fr = new FeatureRenderer(av);\r
+ sr = new SequenceRenderer(av);\r
+ setLayout(new BorderLayout());\r
+ PaintRefresher.Register(this, av.alignment);\r
+ setBackground(Color.white);\r
+ }\r
\r
- AlignViewport av;\r
+ MCview.PDBCanvas pdbCanvas;\r
+ public SequenceRenderer getSequenceRenderer()\r
+ {\r
+ return sr;\r
+ }\r
\r
- public boolean paintFlag = false;\r
+ public FeatureRenderer getFeatureRenderer()\r
+ {\r
+ return fr;\r
+ }\r
\r
- boolean showScores = false;\r
- boolean displaySearch = false;\r
- int [] searchResults = null;\r
+ public void setPDBCanvas(MCview.PDBCanvas pc)\r
+ {\r
+ pdbCanvas = pc;\r
+ }\r
\r
- int chunkHeight;\r
- int chunkWidth;\r
+ public AlignViewport getViewport()\r
+ {\r
+ return av;\r
+ }\r
\r
\r
- public SeqCanvas(AlignViewport av)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ * @param startx DOCUMENT ME!\r
+ * @param endx DOCUMENT ME!\r
+ * @param ypos DOCUMENT ME!\r
+ */\r
+ void drawNorthScale(Graphics g, int startx, int endx, int ypos)\r
{\r
- this.av = av;\r
- fr = new FeatureRenderer(av);\r
- setLayout(new BorderLayout());\r
- PaintRefresher.Register(this);\r
+ int scalestartx = startx - (startx % 10) + 10;\r
\r
+ g.setColor(Color.black);\r
+\r
+ // NORTH SCALE\r
+ for (int i = scalestartx; i < endx; i += 10)\r
+ {\r
+ String string = String.valueOf(i);\r
+ g.drawString(string, (i - startx - 1) * av.charWidth,\r
+ ypos - (av.charHeight / 2));\r
+\r
+ g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),\r
+ (ypos + 2) - (av.charHeight / 2),\r
+ ((i - startx - 1) * av.charWidth) + (av.charWidth / 2), ypos -\r
+ 2);\r
+ }\r
}\r
\r
- public void drawScale(Graphics g, int startx, int endx,int ypos) {\r
- int scalestartx = startx - startx%10 + 10;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ * @param startx DOCUMENT ME!\r
+ * @param endx DOCUMENT ME!\r
+ * @param ypos DOCUMENT ME!\r
+ */\r
+ void drawWestScale(Graphics g, int startx, int endx, int ypos)\r
+ {\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+ ypos += av.charHeight;\r
\r
- g.setColor(Color.black);\r
+ // EAST SCALE\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ {\r
+ SequenceI seq = av.alignment.getSequenceAt(i);\r
+ int index = startx;\r
+ int value = -1;\r
\r
- for (int i=scalestartx;i < endx;i+= 10)\r
- {\r
- String string = String.valueOf(i);\r
- g.drawString(string,(i-startx-1)*av.charWidth,ypos - av.charHeight/2);\r
+ while (index < endx)\r
+ {\r
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
+ {\r
+ index++;\r
\r
- g.drawLine( (i-startx-1)*av.charWidth +av.charWidth/2, ypos+2 - av.charHeight/2,\r
- (i-startx-1)*av.charWidth +av.charWidth/2, ypos-2 );\r
+ continue;\r
+ }\r
\r
- }\r
+ value = av.alignment.getSequenceAt(i).findPosition(index);\r
\r
- }\r
+ break;\r
+ }\r
\r
+ if (value != -1)\r
+ {\r
+ int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))-av.charWidth/2;\r
+ g.drawString(value + "", x,\r
+ (ypos + (i * av.charHeight)) - (av.charHeight / 5));\r
+ }\r
+ }\r
+ }\r
\r
-public void fastPaint(int horizontal, int vertical)\r
-{\r
- if (horizontal == 0 && vertical == 0)\r
- return;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ * @param startx DOCUMENT ME!\r
+ * @param endx DOCUMENT ME!\r
+ * @param ypos DOCUMENT ME!\r
+ */\r
+ void drawEastScale(Graphics g, int startx, int endx, int ypos)\r
+ {\r
+ ypos += av.charHeight;\r
+\r
+ // EAST SCALE\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ {\r
+ SequenceI seq = av.alignment.getSequenceAt(i);\r
+ int index = endx;\r
+ int value = -1;\r
+\r
+ while (index > startx)\r
+ {\r
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
+ {\r
+ index--;\r
+\r
+ continue;\r
+ }\r
+\r
+ value = av.alignment.getSequenceAt(i).findPosition(index);\r
+\r
+ break;\r
+ }\r
+\r
+ if (value != -1)\r
+ {\r
+ g.drawString(String.valueOf(value), av.charWidth/2,\r
+ (ypos + (i * av.charHeight)) - (av.charHeight / 5));\r
+ }\r
+ }\r
+ }\r
\r
- if (img == null || paintFlag)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param horizontal DOCUMENT ME!\r
+ * @param vertical DOCUMENT ME!\r
+ */\r
+ public void fastPaint(int horizontal, int vertical)\r
{\r
- repaint();\r
- return;\r
+ if (gg == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ gg.copyArea(horizontal * av.charWidth,\r
+ vertical * av.charHeight,\r
+ imgWidth,\r
+ imgHeight,\r
+ -horizontal * av.charWidth,\r
+ -vertical * av.charHeight);\r
+\r
+ int sr = av.startRes;\r
+ int er = av.endRes;\r
+ int ss = av.startSeq;\r
+ int es = av.endSeq;\r
+ int transX = 0;\r
+ int transY = 0;\r
+\r
+ if (horizontal > 0) // scrollbar pulled right, image to the left\r
+ {\r
+ er ++;\r
+ transX = (er - sr - horizontal) * av.charWidth;\r
+ sr = er - horizontal;\r
+ }\r
+ else if (horizontal < 0)\r
+ {\r
+ er = sr - horizontal-1;\r
+ }\r
+ else if (vertical > 0) // scroll down\r
+ {\r
+ ss = es - vertical;\r
+\r
+ if (ss < av.startSeq)\r
+ { // ie scrolling too fast, more than a page at a time\r
+ ss = av.startSeq;\r
+ }\r
+ else\r
+ {\r
+ transY = imgHeight - (vertical * av.charHeight);\r
+ }\r
+ }\r
+ else if (vertical < 0)\r
+ {\r
+ es = ss - vertical;\r
+\r
+ if (es > av.endSeq)\r
+ {\r
+ es = av.endSeq;\r
+ }\r
+ }\r
+\r
+ gg.translate(transX, transY);\r
+ drawPanel(gg, sr, er, ss, es, sr, ss, 0);\r
+ gg.translate(-transX, -transY);\r
+\r
+ fastPaint = true;\r
+ repaint();\r
}\r
\r
- gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,\r
- -vertical * av.charHeight);\r
+ /**\r
+ * Definitions of startx and endx (hopefully):\r
+ * SMJS This is what I'm working towards!\r
+ * startx is the first residue (starting at 0) to display.\r
+ * endx is the last residue to display (starting at 0).\r
+ * starty is the first sequence to display (starting at 0).\r
+ * endy is the last sequence to display (starting at 0).\r
+ * NOTE 1: The av limits are set in setFont in this class and\r
+ * in the adjustment listener in SeqPanel when the scrollbars move.\r
+ */\r
+\r
+ // Set this to false to force a full panel paint\r
+ public void paintComponent(Graphics g)\r
+ {\r
+ super.paintComponent(g);\r
+\r
+ sr.renderGaps(av.renderGaps);\r
+\r
+ if ( img != null && (fastPaint\r
+ || (getVisibleRect().width != g.getClipBounds().width)\r
+ || (getVisibleRect().height != g.getClipBounds().height)))\r
+ {\r
+ g.drawImage(img, 0, 0, this);\r
+ fastPaint = false;\r
+ return;\r
+ }\r
+\r
+\r
+ // this draws the whole of the alignment\r
+ imgWidth = getWidth();\r
+ imgHeight = getHeight();\r
+\r
+ imgWidth -= (imgWidth % av.charWidth);\r
+ imgHeight -= (imgHeight % av.charHeight);\r
+\r
+ if ((imgWidth < 1) || (imgHeight < 1))\r
+ {\r
+ return;\r
+ }\r
+\r
+ img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);\r
+ gg = (Graphics2D) img.getGraphics();\r
+ gg.setFont(av.getFont());\r
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
+\r
+ gg.setColor(Color.white);\r
+ gg.fillRect(0, 0, imgWidth, imgHeight);\r
+\r
+\r
+ if (av.getWrapAlignment())\r
+ {\r
+ drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);\r
+ }\r
+ else\r
+ {\r
+ drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq,\r
+ av.startRes, av.startSeq, 0);\r
+ }\r
+\r
+ g.drawImage(img, 0, 0, this);\r
+\r
+ if (pdbCanvas != null)\r
+ {\r
+ pdbCanvas.updateSeqColours();\r
+ }\r
+\r
+ }\r
\r
- int sr = av.startRes, er = av.endRes + 1, ss = av.startSeq, es = av.endSeq,\r
- transX = 0, transY = 0;\r
- if (horizontal > 0) // scrollbar pulled right, image to the left\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param cwidth DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getWrappedCanvasWidth(int cwidth)\r
{\r
- transX = (er - sr - horizontal) * av.charWidth;\r
- sr = er - horizontal;\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+\r
+ LABEL_EAST = 0;\r
+ LABEL_WEST = 0;\r
+\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ LABEL_EAST = fm.stringWidth(getMask()+"0");\r
+ }\r
+\r
+ if (av.scaleLeftWrapped)\r
+ {\r
+ LABEL_WEST = fm.stringWidth(getMask());\r
+ }\r
+\r
+ return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
}\r
- else if (horizontal < 0)\r
- er = sr - horizontal;\r
\r
- else if (vertical > 0) // scroll down\r
+\r
+ /**\r
+ * Generates a string of zeroes.\r
+ * @return String\r
+ */\r
+ String getMask()\r
{\r
- transY = imgHeight - vertical * av.charHeight;\r
- ss = es - vertical;\r
+ String mask = "0";\r
+ for (int i = av.alignment.getWidth(); i > 0; i /= 10)\r
+ {\r
+ mask += "0";\r
+ }\r
+ return mask;\r
}\r
- else if (vertical < 0)\r
- es = ss - vertical;\r
\r
- gg.translate(transX, transY);\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ * @param canvasWidth DOCUMENT ME!\r
+ * @param canvasHeight DOCUMENT ME!\r
+ * @param startRes DOCUMENT ME!\r
+ */\r
+ public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,\r
+ int startRes)\r
+ {\r
\r
- drawPanel(gg, sr, er, ss, es, sr, ss, 0);\r
+ AlignmentI al = av.getAlignment();\r
\r
- gg.translate( -transX, -transY);\r
- getGraphics().drawImage(img, 0, 0, this);\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
\r
-}\r
+ int LABEL_EAST = 0;\r
\r
-/**\r
- * Definitions of startx and endx (hopefully):\r
- * SMJS This is what I'm working towards!\r
- * startx is the first residue (starting at 0) to display.\r
- * endx is the last residue to display (starting at 0).\r
- * starty is the first sequence to display (starting at 0).\r
- * endy is the last sequence to display (starting at 0).\r
- * NOTE 1: The av limits are set in setFont in this class and\r
- * in the adjustment listener in SeqPanel when the scrollbars move.\r
- */\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ LABEL_EAST = fm.stringWidth(getMask()+"0");\r
+ }\r
+\r
+ int LABEL_WEST = 0;\r
\r
- public void paintComponent(Graphics g)\r
- {\r
- // this draws the whole of the alignment\r
- imgWidth = getWidth();\r
- imgHeight = getHeight();\r
+ if (av.scaleLeftWrapped)\r
+ {\r
+ LABEL_WEST = fm.stringWidth(getMask());\r
+ }\r
\r
- imgWidth -= imgWidth%av.charWidth;\r
- imgHeight-= imgHeight%av.charHeight;\r
+ int hgap = av.charHeight;\r
+ if(av.scaleAboveWrapped)\r
+ hgap += av.charHeight;\r
\r
- img = createImage(imgWidth,imgHeight);\r
- gg = (Graphics2D)img.getGraphics();\r
- gg.setFont(av.getFont());\r
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);\r
- paintFlag = false;\r
+ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
+ int cHeight = av.getAlignment().getHeight() * av.charHeight;\r
\r
- gg.setColor(Color.white);\r
- gg.fillRect(0,0,imgWidth,imgHeight);\r
+ av.setWrappedWidth(cWidth);\r
\r
- chunkWidth = getWidth()/av.charWidth;\r
- chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;\r
+ av.endRes = av.startRes + cWidth;\r
\r
- av.setChunkHeight(chunkHeight);\r
- av.setChunkWidth(chunkWidth);\r
\r
+ int endx = (startRes + cWidth) - 1;\r
+ int ypos = hgap;\r
\r
- if (av.getWrapAlignment())\r
- drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);\r
- else\r
- drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes, av.startSeq, 0);\r
\r
- g.setColor(Color.white);\r
- g.fillRect(0,0,getWidth(),getHeight());\r
- g.drawImage(img,0,0,this);\r
+ while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))\r
+ {\r
+ g.setFont(av.getFont());\r
+ g.setColor(Color.black);\r
\r
- }\r
+ if (av.scaleLeftWrapped)\r
+ {\r
+ drawWestScale(g, startRes, endx, ypos);\r
+ }\r
\r
- public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)\r
- {\r
- AlignmentI da = av.getAlignment();\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ g.translate(canvasWidth - LABEL_EAST, 0);\r
+ drawEastScale(g, startRes, endx, ypos);\r
+ g.translate(-(canvasWidth - LABEL_EAST), 0);\r
+ }\r
\r
- int cWidth = canvasWidth/av.charWidth;\r
- int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;\r
+ g.translate(LABEL_WEST, 0);\r
\r
- int endx = startRes+cWidth-1;\r
- int ypos = 2*av.charHeight;\r
+ if (av.scaleAboveWrapped)\r
+ {\r
+ drawNorthScale(g, startRes, endx, ypos);\r
+ }\r
\r
- while (ypos <= canvasHeight)\r
- {\r
- drawScale(g, startRes, endx, ypos);\r
- drawPanel(g, startRes, endx, 0, da.getHeight(), startRes, 0, ypos);\r
+ // When printing we have an extra clipped region,\r
+ // the Printable page which we need to account for here\r
+ Shape clip = g.getClip();\r
\r
- ypos += cHeight;\r
- startRes += cWidth;\r
- endx = startRes + cWidth - 1;\r
+ if (clip == null)\r
+ {\r
+ g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);\r
+ }\r
+ else\r
+ {\r
+ g.setClip(0, (int) clip.getBounds().getY(),\r
+ cWidth * av.charWidth, (int) clip.getBounds().getHeight());\r
+ }\r
\r
- if (endx > da.getWidth())\r
- endx = da.getWidth();\r
- }\r
+ if (av.vconsensus!=null && av.alignment.getWidth() >= av.vconsensus.size())\r
+ {\r
+ endx = av.vconsensus.size() - 2;\r
+ }\r
\r
- }\r
\r
+ drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);\r
\r
- public void drawPanel(Graphics g1,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {\r
+ if(av.showAnnotation)\r
+ {\r
+ g.translate(0, cHeight + ypos + 3);\r
+ if(annotations==null)\r
+ annotations = new AnnotationPanel(av);\r
\r
+ annotations.drawComponent( (Graphics2D) g, startRes, endx + 1);\r
+ g.translate(0, -cHeight - ypos);\r
+ }\r
+ g.setClip(clip);\r
+ g.translate(-LABEL_WEST, 0);\r
\r
- Graphics2D g = (Graphics2D)g1;\r
- g.setFont(av.getFont());\r
- RendererI sr = av.getRenderer();\r
+ ypos += cHeight+getAnnotationHeight()+hgap;\r
+ if(av.showAnnotation)\r
+ ypos -= 3;\r
\r
- /*Vector pid = av.getConsensus(false);\r
- Vector tmpseq = new Vector();\r
- for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
- if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i)))\r
- tmpseq.addElement(av.getAlignment().getSequenceAt(i));\r
+ startRes += cWidth;\r
+ endx = (startRes + cWidth) - 1;\r
\r
- if (sr instanceof SequenceRenderer)\r
- pid = AAFrequency.calculate(tmpseq,x1,x2);\r
+ if (endx > al.getWidth())\r
+ {\r
+ endx = al.getWidth();\r
+ }\r
+ }\r
+ }\r
\r
- else if (sr instanceof GraphRenderer)\r
- pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0),\r
- av.getAlignment().getSequences(),\r
- av.getPIDWindow(),x1,x2);\r
+ AnnotationPanel annotations;\r
+ int getAnnotationHeight()\r
+ {\r
+ if(!av.showAnnotation)\r
+ return 0;\r
\r
-*/\r
+ if(annotations==null)\r
+ annotations = new AnnotationPanel(av);\r
\r
- /* if (y2 > starty && y1 < av.getEndSeq())\r
+ return annotations.adjustPanelHeight();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g1 DOCUMENT ME!\r
+ * @param x1 DOCUMENT ME!\r
+ * @param x2 DOCUMENT ME!\r
+ * @param y1 DOCUMENT ME!\r
+ * @param y2 DOCUMENT ME!\r
+ * @param startx DOCUMENT ME!\r
+ * @param starty DOCUMENT ME!\r
+ * @param offset DOCUMENT ME!\r
+ */\r
+\r
+ float aaRatio = 2f/3f;\r
+ public void increaseAARatio()\r
{\r
- fillBackground(g,\r
- Color.red,\r
- (x1-startx)*charWidth,\r
- offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()),\r
- (x2-x1+1)*charWidth,\r
- offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight()));\r
- }*/\r
-\r
- SequenceI nextSeq;\r
-\r
- /// First draw the sequences\r
- /////////////////////////////\r
- for (int i = y1 ; i < y2 ;i++)\r
+ aaRatio += .025;\r
+ if(aaRatio>1)\r
+ aaRatio = 1;\r
+\r
+ repaint();\r
+ }\r
+\r
+ public void decreaseAARation()\r
{\r
- nextSeq = av.getAlignment().getSequenceAt(i);\r
-\r
- sr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ),x1,x2,\r
- (x1 - startx) * av.charWidth,\r
- offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
- av.charWidth,av.charHeight,null, i);\r
-\r
- if(av.showSequenceFeatures)\r
- {\r
- fr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ), x1, x2,\r
- (x1 - startx) * av.charWidth,\r
- offset +\r
- AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
- av.charWidth, av.charHeight, null, i);\r
- }\r
+ aaRatio -= .025;\r
+ if(aaRatio<0)\r
+ aaRatio = 0;\r
+\r
+ repaint();\r
}\r
- //\r
- /////////////////////////////////////\r
\r
- // Now outline any areas if necessary\r
- /////////////////////////////////////\r
- SequenceGroup group = av.getSelectionGroup();\r
- java.util.Vector groups = av.alignment.getGroups();\r
\r
- int sx = -1, sy = -1, ex = -1;\r
- int groupIndex = -1;\r
- if (group == null && groups.size() > 0)\r
+ synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,\r
+ int y2, int startx, int starty, int offset)\r
{\r
- group = (SequenceGroup) groups.elementAt(0);\r
- groupIndex = 0;\r
- }\r
+ Graphics2D g = (Graphics2D) g1;\r
+ g.setFont(av.getFont());\r
\r
- if (group != null)\r
- do\r
+ SequenceI nextSeq, dna = null;\r
+ int aaHeight = av.charHeight, dnaHeight = av.charHeight;\r
+ Font dnafont = null, aafont = av.getFont();\r
+\r
+ /* if (av.getShowTranslation())\r
{\r
- int oldY = -1;\r
- int i = 0;\r
- boolean inGroup = false;\r
- for (i = y1; i < y2; i++)\r
+ aaHeight = (int) (av.getCharHeight() * aaRatio);\r
+ dnaHeight = (int) (av.getCharHeight() * (1 - aaRatio));\r
+ java.awt.geom.AffineTransform transform = new java.awt.geom.AffineTransform();\r
+ transform.scale(1f / 3f, 1);\r
+ dnafont = new Font(av.getFont().getName(), av.getFont().getStyle(),\r
+ dnaHeight);\r
+ dnafont = dnafont.deriveFont(transform);\r
+\r
+ aafont = new Font(av.getFont().getName(), av.getFont().getStyle(),\r
+ aaHeight);\r
+ transform = new java.awt.geom.AffineTransform();\r
+ transform.scale(1 / aaRatio, 1);\r
+ aafont = aafont.deriveFont(transform);\r
+ }\r
+*/\r
+\r
+ ColourSchemeI cs = av.getGlobalColourScheme();\r
+\r
+ /// First draw the sequences\r
+ /////////////////////////////\r
+ for (int i = y1; i < y2; i++)\r
{\r
- sx = (group.getStartRes() - startx) * av.charWidth;\r
- sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);\r
- ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth;\r
-\r
- if (group.sequences.contains(av.alignment.getSequenceAt(i))\r
- && sx < getWidth()\r
- && ex > 0)\r
- {\r
- if (!inGroup)\r
+ nextSeq = av.alignment.getSequenceAt(i);\r
+ g.setFont(aafont);\r
+ /* if(av.getShowTranslation())\r
{\r
- oldY = sy;\r
- inGroup = true;\r
- if (group == av.getSelectionGroup())\r
- {\r
- // g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND, 3f, new float[]{5f,2f,2f}, 0f ));\r
- g.setColor(Color.RED);\r
- }\r
- else\r
+ dna = nextSeq;\r
+ StringBuffer sb = new StringBuffer();\r
+ for(int r = 0; r<nextSeq.getLength(); r+=3)\r
{\r
- g.setStroke(new BasicStroke());\r
- g.setColor(group.getOutlineColour());\r
+ String codon = nextSeq.getSequence(r, r+3);\r
+ codon = codon.replace('U', 'T');\r
+ String res = ResidueProperties.codonTranslate(codon);\r
+ if(res !=null )\r
+ {\r
+ if (res.equals("STOP"))\r
+ sb.append("X");\r
+ else\r
+ sb.append(res);\r
+ }\r
}\r
- }\r
- }\r
- else\r
- {\r
- if (inGroup)\r
+ nextSeq = new Sequence("d", sb.toString());\r
+ }*/\r
+\r
+ sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),\r
+ x1, x2, (x1 - startx) * av.charWidth,\r
+ offset + ( (i - starty) * av.charHeight), av.charWidth,\r
+ aaHeight);\r
+\r
+ /* if(av.getShowTranslation())\r
+ {\r
+ av.setGlobalColourScheme(new NucleotideColourScheme());\r
+ g.setFont(dnafont);\r
+ sr.drawSequence(g, dna, null,\r
+ x1*3, (x2+2) * 3, ( (x1 - startx) * av.charWidth) / 3,\r
+ offset + ( (i - starty) * av.charHeight) + aaHeight,\r
+ av.charWidth / 3,\r
+ dnaHeight);\r
+ av.setGlobalColourScheme(cs);\r
+ }*/\r
+\r
+ if (av.showSequenceFeatures)\r
{\r
- g.drawRect(sx, oldY, ex, (sy - oldY));\r
- inGroup = false;\r
+ fr.drawSequence(g, nextSeq, x1, x2,\r
+ (x1 - startx) * av.charWidth,\r
+ offset + ((i - starty) * av.charHeight), av.charWidth,\r
+ av.charHeight);\r
}\r
- }\r
}\r
- if (inGroup)\r
- {\r
- sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);\r
- g.drawRect(sx, oldY, ex, (sy - oldY));\r
- inGroup = false;\r
- }\r
-\r
- groupIndex++;\r
- if (groupIndex >= groups.size())\r
- break;\r
\r
- group = (SequenceGroup) groups.elementAt(groupIndex);\r
-\r
- }\r
- while (groupIndex < groups.size());\r
+ //\r
+ /////////////////////////////////////\r
+ // Now outline any areas if necessary\r
+ /////////////////////////////////////\r
+ SequenceGroup group = av.getSelectionGroup();\r
\r
+ int sx = -1;\r
+ int sy = -1;\r
+ int ex = -1;\r
+ int groupIndex = -1;\r
\r
- /// Highlight search Results once all sequences have been drawn\r
- //////////////////////////////////////////////////////////\r
- if(displaySearch)\r
- {\r
- for(int r=0; r<searchResults.length; r+=3)\r
- {\r
- int searchSeq = searchResults[r];\r
- int searchStart = searchResults[r+1];\r
- int searchEnd = searchResults[r+2];\r
+ if ((group == null) && (av.alignment.getGroups().size() > 0))\r
+ {\r
+ group = (SequenceGroup) av.alignment.getGroups().elementAt(0);\r
+ groupIndex = 0;\r
+ }\r
\r
- if (searchSeq >= y1 && searchSeq < y2)\r
+ if (group != null)\r
{\r
- SequenceRenderer ssr = (SequenceRenderer) sr;\r
- ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq),\r
- searchStart,\r
- searchEnd,\r
- (searchStart - startx) * av.charWidth,\r
- offset +\r
- AlignmentUtil.getPixelHeight(starty, searchSeq,\r
- av.charHeight),\r
- av.charWidth,\r
- av.charHeight);\r
+ do\r
+ {\r
+ int oldY = -1;\r
+ int i = 0;\r
+ boolean inGroup = false;\r
+ int top = -1;\r
+ int bottom = -1;\r
+\r
+ for (i = y1; i < y2; i++)\r
+ {\r
+ sx = (group.getStartRes() - startx) * av.charWidth;\r
+ sy = offset + ((i - starty) * av.charHeight);\r
+ ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -\r
+ 1;\r
+\r
+ if(sx+ex<0 || sx>imgWidth)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if ( (sx <= (x2-x1)*av.charWidth) &&\r
+ group.sequences.contains(av.alignment.getSequenceAt(\r
+ i)))\r
+ {\r
+ if ((bottom == -1) &&\r
+ !group.sequences.contains(\r
+ av.alignment.getSequenceAt(i + 1)))\r
+ {\r
+ bottom = sy + av.charHeight;\r
+ }\r
+\r
+ if (!inGroup)\r
+ {\r
+ if (((top == -1) && (i == 0)) ||\r
+ !group.sequences.contains(\r
+ av.alignment.getSequenceAt(i - 1)))\r
+ {\r
+ top = sy;\r
+ }\r
+\r
+ oldY = sy;\r
+ inGroup = true;\r
+\r
+ if (group == av.getSelectionGroup())\r
+ {\r
+ g.setStroke(new BasicStroke(1,\r
+ BasicStroke.CAP_BUTT,\r
+ BasicStroke.JOIN_ROUND, 3f,\r
+ new float[] { 5f, 3f }, 0f));\r
+ g.setColor(Color.RED);\r
+ }\r
+ else\r
+ {\r
+ g.setStroke(new BasicStroke());\r
+ g.setColor(group.getOutlineColour());\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (inGroup)\r
+ {\r
+ if (sx >= 0 && sx < imgWidth)\r
+ g.drawLine(sx, oldY, sx, sy);\r
+\r
+ if (sx + ex < imgWidth)\r
+ g.drawLine(sx + ex, oldY, sx + ex, sy);\r
+\r
+ if (sx < 0)\r
+ {\r
+ ex += sx;\r
+ sx = 0;\r
+ }\r
+\r
+ if (sx + ex > imgWidth)\r
+ ex = imgWidth;\r
+\r
+ else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)\r
+ ex = (x2 - x1 + 1) * av.charWidth;\r
+\r
+ if (top != -1)\r
+ {\r
+ g.drawLine(sx, top, sx + ex, top);\r
+ top = -1;\r
+ }\r
+\r
+ if (bottom != -1)\r
+ {\r
+ g.drawLine(sx, bottom, sx + ex, bottom);\r
+ bottom = -1;\r
+ }\r
+\r
+ inGroup = false;\r
+ }\r
+ }\r
+ }\r
+\r
+ if (inGroup)\r
+ {\r
+ sy = offset + ( (i - starty) * av.charHeight);\r
+ if (sx >= 0 && sx < imgWidth)\r
+ g.drawLine(sx, oldY, sx, sy);\r
+\r
+ if (sx + ex < imgWidth)\r
+ g.drawLine(sx + ex, oldY, sx + ex, sy);\r
+\r
+ if (sx < 0)\r
+ {\r
+ ex += sx;\r
+ sx = 0;\r
+ }\r
+\r
+ if (sx + ex > imgWidth)\r
+ ex = imgWidth;\r
+ else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)\r
+ ex = (x2 - x1 + 1) * av.charWidth;\r
+\r
+ if (top != -1)\r
+ {\r
+ g.drawLine(sx, top, sx + ex, top);\r
+ top = -1;\r
+ }\r
+\r
+ if (bottom != -1)\r
+ {\r
+ g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);\r
+ bottom = -1;\r
+ }\r
+\r
+ inGroup = false;\r
+ }\r
+\r
+ groupIndex++;\r
+\r
+ if (groupIndex >= av.alignment.getGroups().size())\r
+ {\r
+ break;\r
+ }\r
+\r
+ group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);\r
+ }\r
+ while (groupIndex < av.alignment.getGroups().size());\r
}\r
- }\r
- }\r
\r
- }\r
+ /// Highlight search Results once all sequences have been drawn\r
+ //////////////////////////////////////////////////////////\r
+ if (displaySearch)\r
+ {\r
+ for (int r = 0; r < searchResults.length; r += 3)\r
+ {\r
+ int searchSeq = searchResults[r];\r
\r
+ if ((searchSeq >= y1) && (searchSeq < y2))\r
+ {\r
+ SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);\r
\r
- public int getChunkWidth() {\r
- return chunkWidth;\r
- }\r
+ int searchStart = seq.findIndex(searchResults[r + 1]) - 1;\r
+ int searchEnd = seq.findIndex(searchResults[r + 2]) - 1;\r
\r
- public void highlightSearchResults(int [] results)\r
- {\r
- // results are in the order sequence, startRes, endRes\r
- if(results==null)\r
- displaySearch = false;\r
- else\r
- displaySearch = true;\r
+ SequenceRenderer ssr = (SequenceRenderer) sr;\r
\r
- searchResults = results;\r
+ if (searchStart < x1)\r
+ {\r
+ searchStart = x1;\r
+ }\r
\r
- paintFlag = true;\r
- repaint();\r
- }\r
+ if (searchEnd > x2)\r
+ {\r
+ searchEnd = x2;\r
+ }\r
\r
+ ssr.drawHighlightedText(seq, searchStart, searchEnd,\r
+ (searchStart - startx) * av.charWidth,\r
+ offset + ((searchSeq - starty) * av.charHeight),\r
+ av.charWidth, av.charHeight);\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param results DOCUMENT ME!\r
+ */\r
+ public void highlightSearchResults(int[] results)\r
+ {\r
+ // results are in the order sequence, startRes, endRes\r
+ if (results == null)\r
+ {\r
+ displaySearch = false;\r
+ }\r
+ else\r
+ {\r
+ displaySearch = true;\r
+ }\r
+\r
+ searchResults = results;\r
+\r
+ repaint();\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff