X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=b961b2c8d894c24b23b38ea4434ec4fa515a2a93;hb=783520af519c958e10a2af29f1d4242e1ab890a3;hp=7a52bcc7b82803a496931cb4e56b3ba70d7cb4dc;hpb=526094d494484bfa89f9659fccf83a37b8c19829;p=jalview.git diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java index 7a52bcc..b961b2c 100755 --- a/src/jalview/gui/SequenceRenderer.java +++ b/src/jalview/gui/SequenceRenderer.java @@ -1,124 +1,353 @@ +/* + * 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 jalview.schemes.*; import java.awt.*; -import java.util.*; -public class SequenceRenderer implements RendererI + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class SequenceRenderer { - FontMetrics fm; + AlignViewport av; + FontMetrics fm; + boolean renderGaps = true; + SequenceGroup currentSequenceGroup = null; + SequenceGroup[] allGroups = null; + Color resBoxColour; + Graphics graphics; - public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) { + /** + * Creates a new SequenceRenderer object. + * + * @param av DOCUMENT ME! + */ + public SequenceRenderer(AlignViewport av) + { + this.av = av; + } - Color c = cs.findColour(seq, seq.getSequence(i, i + 1), i, null); - return c; + /** + * DOCUMENT ME! + * + * @param b DOCUMENT ME! + */ + public void renderGaps(boolean b) + { + renderGaps = b; + } - } + /** + * DOCUMENT ME! + * + * @param cs DOCUMENT ME! + * @param seq DOCUMENT ME! + * @param i DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) + { + getBoxColour(cs, seq, i); + return resBoxColour; + } - public void drawSequence(Graphics g,ColourSchemeI cs,SequenceI seq,int start, int end, int x1, int y1, double width, int height,boolean showScores, boolean displayBoxes, boolean displayText, boolean colourText,Vector freq, int seqnum) { + /** + * DOCUMENT ME! + * + * @param cs DOCUMENT ME! + * @param seq DOCUMENT ME! + * @param i DOCUMENT ME! + */ + void getBoxColour(ColourSchemeI cs, SequenceI seq, int i) + { + if (cs != null) + { + resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i); + } + else + { + resBoxColour = Color.white; + } + } + /** + * DOCUMENT ME! + * + * @param g DOCUMENT ME! + * @param seq DOCUMENT ME! + * @param sg DOCUMENT ME! + * @param start DOCUMENT ME! + * @param end DOCUMENT ME! + * @param x1 DOCUMENT ME! + * @param y1 DOCUMENT ME! + * @param width DOCUMENT ME! + * @param height DOCUMENT ME! + */ + public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg, + int start, int end, int x1, int y1, int width, int height) + { + allGroups = sg; - if (displayBoxes) - drawBoxes(g,cs,seq,start,end,x1,y1,(int)width, height,freq); + graphics = g; + + drawBoxes(seq, start, end, x1, y1, (int) width, height); - if (displayText) - { fm = g.getFontMetrics(); - drawText(g,cs,colourText,seq,start,end,x1,y1,(int)width,height); + drawText(seq, start, end, x1, y1, (int) width, height); } - } - - public void drawBoxes(Graphics g,ColourSchemeI cs, SequenceI seq,int start, int end, int x1, int y1, int width, int height,Vector freq) { - int i = start; - int length = seq.getLength(); - - Color currentColor = Color.WHITE; - - int curStart = x1; - int curWidth = width; - - // int threshold = 80; - - while (i <= end && i < length) { - Color c = getResidueBoxColour(cs,seq,i); - - // Hashtable hash = (Hashtable)freq.elementAt(i-start); - // String s = (String)hash.get("maxResidue"); - // int count = ((Integer)hash.get("maxCount")).intValue(); - // int max = ((Integer)hash.get("size")).intValue(); - // int nongap = ((Integer)hash.get("nongap")).intValue(); - // float frac = (float)(count*1.0/(1.0*nongap)); - - //System.out.println("Frac/count/nongap " + frac + " " + count + " " + nongap); - /* if (!seq.getSequence().substring(i,i+1).equals(s) || - s.equals("-") || - s.equals(".") || - s.equals(" ")) - { - c = Color.white; - } else { - if (frac > 0.9) { - c = Color.red; - } else if (frac > 0.8) { - c = Color.orange; - } else if (frac > 0.7) { - c = Color.pink; - } else if (frac > 0.5) { - c = Color.yellow; - } else if (frac> 0.3) { - c = Color.lightGray; - } - }*/ - - if (c != currentColor || c != null) - { - g.fillRect(x1+width*(curStart-start),y1,curWidth,height); - - currentColor = c; - g.setColor(c); - - curStart = i; - curWidth = width; - } - else - curWidth += width; - - i++; + + /** + * DOCUMENT ME! + * + * @param seq DOCUMENT ME! + * @param start DOCUMENT ME! + * @param end DOCUMENT ME! + * @param x1 DOCUMENT ME! + * @param y1 DOCUMENT ME! + * @param width DOCUMENT ME! + * @param height DOCUMENT ME! + */ + public void drawBoxes(SequenceI seq, int start, int end, int x1, int y1, + int width, int height) + { + int i = start; + int length = seq.getLength(); + + int curStart = -1; + int curWidth = width; + + Color tempColour = null; + + while (i <= end) + { + resBoxColour = Color.white; + + if (i < length) + { + if (inCurrentSequenceGroup(i)) + { + if (currentSequenceGroup.getDisplayBoxes()) + { + getBoxColour(currentSequenceGroup.cs, seq, i); + } + } + else if (av.getShowBoxes()) + { + getBoxColour(av.getGlobalColourScheme(), seq, i); + } + + } + + if (resBoxColour != tempColour) + { + if (tempColour != null) + { + int xxx = x1 + (int) (av.charWidth * (curStart - start)); + if (width != av.charWidth) + { + xxx = x1 + (int) (av.charWidth * (curStart - start)) / 3; + } + + + graphics.fillRect(xxx, y1, + curWidth, height); + } + + graphics.setColor(resBoxColour); + + curStart = i; + curWidth = width; + tempColour = resBoxColour; + } + else + { + curWidth += width; + } + + i++; + } + + int xxx = x1 + (int) (av.charWidth * (curStart - start)); + if (width != av.charWidth) + { + xxx = x1 + (int) (av.charWidth * (curStart - start)) / 3; + } + + + graphics.fillRect(xxx, y1, curWidth, + height); } - g.fillRect(x1+width*(curStart-start),y1,curWidth,height); - } - - public void drawText(Graphics g, ColourSchemeI cs, boolean colText, SequenceI seq,int start, int end, int x1, int y1, int width, int height) - { - int pady = height/5; - int charOffset=0; - g.setColor(Color.black); - - char s; - // Need to find the sequence position here. - for (int i = start; i <= end; i++) + + /** + * DOCUMENT ME! + * + * @param seq DOCUMENT ME! + * @param start DOCUMENT ME! + * @param end DOCUMENT ME! + * @param x1 DOCUMENT ME! + * @param y1 DOCUMENT ME! + * @param width DOCUMENT ME! + * @param height DOCUMENT ME! + */ + public void drawText(SequenceI seq, int start, int end, int x1, int y1, + int width, int height) { - if (i < end && i < seq.getLength()) - s = seq.getSequence().charAt(i); - else if(i=seq.getLength()) + end = seq.getLength()-1; + + for (int i = start; i <= end; i++) { - Color c = getResidueBoxColour(cs, seq, i); - g.setColor(c.darker()); + graphics.setColor(Color.black); + + s = sequence.charAt(i); + + if (!renderGaps && jalview.util.Comparison.isGap(s)) + { + continue; + } + + if (inCurrentSequenceGroup(i)) + { + if (!currentSequenceGroup.getDisplayText()) + { + continue; + } + + if (currentSequenceGroup.getColourText()) + { + getBoxColour(currentSequenceGroup.cs, seq, i); + graphics.setColor(resBoxColour.darker()); + } + } + else + { + if (!av.getShowText()) + { + continue; + } + + if (av.getColourText()) + { + getBoxColour(av.getGlobalColourScheme(), seq, i); + + if (av.getShowBoxes()) + { + graphics.setColor(resBoxColour.darker()); + } + else + { + graphics.setColor(resBoxColour); + } + } + } + + charOffset = (width - fm.charWidth(s)) / 2; + + int xxx = charOffset + x1 + (int)(av.charWidth * (i - start)); + if(width != av.charWidth) + { + xxx = charOffset + x1 + (int)(av.charWidth * (i - start))/3; + } + + graphics.drawString(String.valueOf(s),xxx, (y1 + height) - pady); + } + } + + /** + * DOCUMENT ME! + * + * @param res DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + boolean inCurrentSequenceGroup(int res) + { + if (allGroups == null) + { + return false; } - charOffset = (width - fm.charWidth(s))/2; + for (int i = 0; i < allGroups.length; i++) + { + if ((allGroups[i].getStartRes() <= res) && + (allGroups[i].getEndRes() >= res)) + { + currentSequenceGroup = allGroups[i]; + return true; + } + } - g.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady); + return false; } - } + /** + * DOCUMENT ME! + * + * @param seq DOCUMENT ME! + * @param start DOCUMENT ME! + * @param end DOCUMENT ME! + * @param x1 DOCUMENT ME! + * @param y1 DOCUMENT ME! + * @param width DOCUMENT ME! + * @param height DOCUMENT ME! + */ + public void drawHighlightedText(SequenceI seq, int start, int end, int x1, + int y1, int width, int height) + { + int pady = height / 5; + int charOffset = 0; + graphics.setColor(Color.BLACK); + graphics.fillRect(x1, y1, width * (end - start + 1), height); + graphics.setColor(Color.white); + + char s = '~'; + + // Need to find the sequence position here. + for (int i = start; i <= end; i++) + { + if (i < seq.getLength()) + { + s = seq.getSequence().charAt(i); + } + + charOffset = (width - fm.charWidth(s)) / 2; + graphics.drawString(String.valueOf(s), + charOffset + x1 + (width * (i - start)), (y1 + height) - pady); + } + } }