not used at present

diff --git a/src/jalview/gui/BlockRenderer.java b/src/jalview/gui/BlockRenderer.java
deleted file mode 100755 (executable)
index 1dca1c4..0000000
--- a/src/jalview/gui/BlockRenderer.java
+++ /dev/null
@@ -1,136 +0,0 @@
-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import jalview.analysis.*;\r
-import jalview.util.*;\r
-import java.awt.*;\r
-import java.util.*;\r
-\r
-public class BlockRenderer implements RendererI {\r
-    protected Color   color = Color.black;\r
-    protected Color   maroon = new Color(200,0,50);\r
-    protected Color   purple = new Color(255,100,255);\r
-\r
-    public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) {\r
-       Color c = cs.findColour(seq,seq.getSequence(i,i+1),i,null);\r
-       return c;\r
-    }\r
-\r
-    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,Vector pid, int seqnum,AlignViewport av) {\r
-\r
-/*     int i      = start;\r
-       int length = seq.getLength();\r
-\r
-       Color currentColor = Color.white;\r
-       Vector kmers = av.getKmers();\r
-\r
-       g.setColor(Color.black);\r
-\r
-        int prev = -1;\r
-\r
-       int seqno = -1;\r
-\r
-       for (int ii = 0; ii < av.getAlignment().getHeight(); ii++) {\r
-           if (av.getSelection().contains(av.getAlignment().getSequenceAt(ii))) {\r
-               seqno = ii;\r
-           }\r
-       }\r
-\r
-       int blstart = start - 20;\r
-       int blend   = end   + 20;\r
-\r
-       if (blstart < 0) {\r
-           blstart = 0;\r
-       }\r
-\r
-       if (blend > av.getAlignment().getWidth()) {\r
-           blend = av.getAlignment().getWidth();\r
-       }\r
-\r
-       Hashtable blocks = AAFrequency.findBlocks(av.getAlignment().getSequences(),\r
-                                                 blstart,\r
-                                                 blend,\r
-                                                 av.getSelection().asVector());\r
-\r
-       Hashtable hkmer = AlignmentUtil.findKmers(seq,blstart,blend,kmers);\r
-\r
-       boolean   inblock = false;\r
-\r
-       int       bstart = -1;\r
-       int       blen   = -1;\r
-       int       klen   = -1;\r
-       int       block_end = -1;\r
-       Color bc;\r
-\r
-       // System.out.println("Rendering " + start + " " + end);\r
-\r
-       while (i <= blend && i < length) {\r
-           boolean foundblock = false;\r
-\r
-           if (blocks.get(new Integer(i-blstart)) != null) {\r
-\r
-               blen   = ((Integer)blocks.get(new Integer(i-blstart))).intValue();\r
-\r
-               foundblock = true;\r
-\r
-               block_end = i + blen-1;\r
-\r
-               g.setColor(getColor(blen));\r
-               g.fillRect(x1+(int)(width*(i-start)),y1,\r
-                          (int)width+1,             height/2);\r
-           }\r
-\r
-           boolean foundKmer = false;\r
-\r
-           if (hkmer.get(new Integer(i-blstart)) != null) {\r
-\r
-\r
-               klen   = ((Integer)hkmer.get(new Integer(i-blstart))).intValue();\r
-\r
-               //              System.out.println("Got kmer " + i + " " + start + " kength " + klen);\r
-\r
-               foundKmer = true;\r
-\r
-               g.setColor(Color.lightGray);\r
-\r
-               if ((int)width> 5) {\r
-                   g.fillRect(x1+(int)(width*(i-start)),y1+height/2,\r
-                              (int)(width*klen)+1,             height/2);\r
-               } else {\r
-                   g.fillRect(x1+(int)(width*(i-start)),y1+height/2,\r
-                              (int)(width*klen)+1,             height/2);\r
-\r
-               }\r
-\r
-           }\r
-\r
-           if (width > 5) {\r
-               g.setColor(Color.black);\r
-               g.drawString(seq.getSequence().substring(i,i+1),x1+(int)(width*(i-start)),y1+height);\r
-           }\r
-           i++;\r
-       }*/\r
-    }\r
-\r
-    public Color getColor(int blen) {\r
-\r
-       Color bc;\r
-\r
-       if (blen > 20 ) {\r
-           bc = Color.yellow;\r
-       }else if (blen > 10) {\r
-           bc = Color.red;\r
-       } else if (blen > 5) {\r
-           bc = Color.blue;\r
-       } else if (blen > 2) {\r
-           bc = purple;\r
-       } else if (blen == 2) {\r
-           bc = Color.orange;\r
-\r
-       } else {\r
-           bc = Color.lightGray;\r
-       }\r
-       return bc;\r
-    }\r
-}\r

diff --git a/src/jalview/gui/CpGRenderer.java b/src/jalview/gui/CpGRenderer.java
deleted file mode 100755 (executable)
index b5dc128..0000000
--- a/src/jalview/gui/CpGRenderer.java
+++ /dev/null
@@ -1,87 +0,0 @@
-package jalview.gui;\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import jalview.util.*;\r
-import jalview.analysis.*;\r
-import java.awt.*;\r
-import java.awt.geom.*;\r
-import java.util.*;\r
-\r
-public class CpGRenderer implements RendererI {\r
-    protected Color   color = Color.black;\r
-\r
-    public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) {\r
-       Color c = cs.findColour(seq,seq.getSequence(i,i+1),i,null);\r
-       return c;\r
-    }\r
-\r
-    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,Vector pid, int seqnum,AlignViewport av) {\r
-\r
-       int i      = start;\r
-       int length = seq.getLength();\r
-\r
-       Color currentColor = Color.white;\r
-\r
-       g.setColor(Color.black);\r
-\r
-        int window = 1000;\r
-        int max    = window/5;\r
-\r
-        int step = window/10;\r
-\r
-        if (step > window) {\r
-          step = window;\r
-        }\r
-\r
-        if (window < 2) {\r
-           window = 2;\r
-           step = 1;\r
-        }\r
-\r
-        int cpgstart = start;\r
-        int cpgend   = end;\r
-\r
-       if (cpgstart <= window/2 ) {\r
-           cpgstart = window/2;\r
-       }\r
-       if (cpgend+window/2 >= length) {\r
-           cpgend = length-window/2;\r
-       }\r
-\r
-       Hashtable vals = AAFrequency.findKmerCount(seq,cpgstart,cpgend,window,step,av.getKmers());\r
-\r
-       Enumeration en = vals.keys();\r
-\r
-       Vector valset = new Vector();\r
-\r
-       while (en.hasMoreElements()) {\r
-           valset.add((Integer)en.nextElement());\r
-       }\r
-       Collections.sort(valset);\r
-\r
-       g.setColor(Color.black);\r
-\r
-       int j = 0;\r
-\r
-       while (j < valset.size()) {\r
-\r
-           Integer posInt = (Integer)valset.elementAt(j);\r
-           int     count  = ((Integer)vals.get(posInt)).intValue();\r
-           int     pos    = posInt.intValue();\r
-\r
-            if (count > 40) {\r
-               g.setColor(Color.red);\r
-            } else {\r
-               g.setColor(Color.black);\r
-            }\r
-\r
-           g.fillRect(x1 + (int)(width*(pos-start-width/2)),\r
-                      y1+height - (int)(count*height/max),\r
-                      (int)(step*width),\r
-                      (int)(count*height/max));\r
-\r
-           j++;\r
-       }\r
-    }\r
-\r
-}\r

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
deleted file mode 100755 (executable)
index cd754c7..0000000
--- a/src/jalview/gui/FeatureRenderer.java
+++ /dev/null
@@ -1,85 +0,0 @@
-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import java.awt.*;\r
-import java.util.*;\r
-\r
-public class FeatureRenderer implements RendererI {\r
-\r
-\r
-    public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) {\r
-       Color c = cs.findColour(seq,seq.getSequence(i,i+1),i,null);\r
-       return c;\r
-    }\r
-\r
-    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,Vector pid, int seqnum,AlignViewport av) {\r
-\r
-       int i      = start;\r
-       int length = seq.getLength();\r
-\r
-       Color currentColor = Color.black;\r
-\r
-\r
-       int    prev   = -1;\r
-        int    fstart = 0;\r
-        char   prevc   = '-';\r
-\r
-       g.setColor(Color.magenta);\r
-\r
-       while (i <= end && i < length) {\r
-            char c = seq.getCharAt(i);\r
-           if (c != '-') {\r
-\r
-              if (prevc != c) {\r
-\r
-                if (prevc == 'F') {\r
-                  g.setColor(Color.green);\r
-                } else if (prevc == 'R') {\r
-                  g.setColor(Color.cyan);\r
-                } else if (prevc == 'M') {\r
-                  g.setColor(Color.magenta);\r
-                } else if (prevc == 'P') {\r
-                  g.setColor(Color.yellow);\r
-                }\r
-               g.fillRect(x1+(int)(width*(i-fstart)),y1+height/4,(int)((prev-fstart+1)*width),height/2);\r
-\r
-                prevc   = c;\r
-                fstart = i;\r
-            }\r
-          } else if (prevc != '-') {\r
-                if (prevc == 'F') {\r
-                  g.setColor(Color.green);\r
-                } else if (prevc == 'R') {\r
-                  g.setColor(Color.cyan);\r
-                } else if (prevc == 'M') {\r
-                  g.setColor(Color.magenta);\r
-                } else if (prevc == 'P') {\r
-                  g.setColor(Color.yellow);\r
-                }\r
-               g.fillRect(x1+(int)(width*(fstart-start)),y1+height/4,(int)((i-fstart+1)*width),height/2);\r
-\r
-                prevc = c;\r
-          } else {\r
-            fstart = -1;\r
-          }\r
-           i++;\r
-       }\r
-\r
-        if (fstart != -1) {\r
-        if (prevc == 'F') {\r
-          g.setColor(Color.green);\r
-        } else if (prevc == 'R') {\r
-          g.setColor(Color.cyan);\r
-        } else if (prevc == 'M') {\r
-          g.setColor(Color.magenta);\r
-        } else if (prevc == 'P') {\r
-          g.setColor(Color.yellow);\r
-        }\r
-\r
-       //g.fillRect(x1+(int)(width*(fstart-start)),y1+height/4,(int)((end-fstart+1)*width),height/2);\r
-\r
-        }\r
-    }\r
-\r
-}\r

diff --git a/src/jalview/gui/GraphRenderer.java b/src/jalview/gui/GraphRenderer.java
deleted file mode 100755 (executable)
index e7d1757..0000000
--- a/src/jalview/gui/GraphRenderer.java
+++ /dev/null
@@ -1,128 +0,0 @@
-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import jalview.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.geom.*;\r
-import java.util.*;\r
-\r
-public class GraphRenderer implements RendererI {\r
-    protected Color   color = Color.black;\r
-    protected Color   maroon = new Color(200,0,50);\r
-\r
-    public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) {\r
-       Color c = cs.findColour(seq,seq.getSequence(i,i+1),i,null);\r
-       return c;\r
-    }\r
-\r
-    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,Vector pid, int seqnum,AlignViewport av) {\r
-\r
-       int i      = start;\r
-       int length = seq.getLength();\r
-\r
-       Color currentColor = Color.white;\r
-\r
-       g.setColor(Color.black);\r
-\r
-        int prev = -1;\r
-\r
-       while (i <= end && i < length) {\r
-            char c = seq.getCharAt(i);\r
-\r
-            if (c != '-') {\r
-           Vector values = (Vector)pid.elementAt(i-start);\r
-           int val = ((Integer)values.elementAt(seqnum)).intValue();\r
-\r
-           int frac = (int)(100*val/(av.getPIDWindow()+1));\r
-\r
-//         if (frac > 95) {\r
- //               g.setColor(maroon);\r
-  //          } else if (frac > 90) {\r
-//             g.setColor(Color.red);\r
-//         } else if (frac > 80) {\r
-//             g.setColor(Color.orange);\r
-//         } else if (frac > 70) {\r
-//             g.setColor(Color.pink);\r
-//         } else if (frac > 50) {\r
-//             g.setColor(Color.yellow);\r
-//         } else if (frac > 30) {\r
-//             g.setColor(Color.lightGray);\r
-//         }\r
-\r
-            int baseline = av.getPIDBaseline();\r
-\r
-            frac -= baseline;\r
-\r
-            if (frac < 0) {\r
-              frac = 0;\r
-            }\r
-           if (baseline == 100) {\r
-               baseline = 99;\r
-           }\r
-\r
-             Graphics2D g2d = (Graphics2D)g;\r
-\r
-            g2d.setColor(new Color(255*frac/(100-baseline),50*frac/(100-baseline),50*frac/(100-baseline)));\r
-\r
-             //g.setColor(new Color(255*frac/(100-baseline),50*frac/(100-baseline),255-50*frac/(100-baseline)));\r
-            //g.fillRect(x1+(int)(width*(i-start)),y1+height - (int)(frac*height/(100-baseline)),\r
-                          //width,                      (int)(frac*height/(100-baseline)));\r
-\r
-             int[] xpoints = new int[4];\r
-             int[] ypoints = new int[4];\r
-\r
-             if (prev == -1) {\r
-               prev = y1 + height - (int)(frac*height/(100-baseline));\r
-             }\r
-\r
-            //   1----2\r
-            //   |    |\r
-            //   4----3\r
-\r
-            xpoints[0] = (x1+ (int)(width*(i-start)));\r
-             ypoints[0] = prev;\r
-\r
-             xpoints[1] = (x1 + (int)(width*(i-start+1)));\r
-             ypoints[1] = y1 + height - (int)(frac*height/(100-baseline));\r
-\r
-             xpoints[3] = (x1 + (int)(width*(i-start)));;\r
-             ypoints[3] = y1 + height;\r
-\r
-             xpoints[2] = (x1  + (int)(width*(i-start+1)));\r
-             ypoints[2] = y1 + height;\r
-\r
-            Polygon poly = new Polygon();\r
-\r
-            poly.xpoints = xpoints;\r
-            poly.ypoints = ypoints;\r
-            poly.npoints = 4;\r
-\r
-             g2d.fill(poly);\r
-\r
-             if (width > 5) {\r
-                g.setColor(Color.black);\r
-                g.drawString(seq.getSequence().substring(i,i+1),x1+(int)(width*(i-start)),y1+height);\r
-             } else {\r
-                g.setColor(Color.black);\r
-\r
-                if (prev != -1) {\r
-\r
-              g.drawLine(x1+(int)(width*(i-start)-width/2),  prev,\r
-                         x1+(int)(width*(i-start+1)-width/2),y1+height - (int)(frac*height/(100-baseline)));\r
-              } else {\r
-              g.drawLine(x1+(int)(width*(i-start)),  y1+height - (int)(frac*height/(100-baseline)),\r
-                         x1+(int)(width*(i-start+1)),y1+height - (int)(frac*height/(100-baseline)));\r
-              }\r
-\r
-            }\r
-            prev = ypoints[1];\r
-           }  else {\r
-              prev = -1;\r
-            }\r
-           i++;\r
-       }\r
-    }\r
-\r
-}\r