/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
-import java.util.*;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
-import java.awt.*;
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
-import jalview.datamodel.*;
-
-public class ClustalxColourScheme
- extends ResidueColourScheme // implements IParameterizable
+public class ClustalxColourScheme extends ResidueColourScheme // implements
+// IParameterizable
{
public static Hashtable colhash = new Hashtable();
+
Hashtable[] cons;
+
int[][] cons2;
+
ConsensusColour[] colours;
+
ConsensusColour[] ResidueColour;
+
int size;
+
Consensus[] conses = new Consensus[32];
+
Vector colourTable = new Vector();
- private boolean includeGaps=true;
-
+
+ private boolean includeGaps = true;
+
{
- colhash.put("RED", new Color( (float) 0.9, (float) 0.2, (float) 0.1));
- colhash.put("BLUE", new Color( (float) 0.5, (float) 0.7, (float) 0.9));
- colhash.put("GREEN", new Color( (float) 0.1, (float) 0.8, (float) 0.1));
- colhash.put("ORANGE", new Color( (float) 0.9, (float) 0.6, (float) 0.3));
- colhash.put("CYAN", new Color( (float) 0.1, (float) 0.7, (float) 0.7));
- colhash.put("PINK", new Color( (float) 0.9, (float) 0.5, (float) 0.5));
- colhash.put("MAGENTA", new Color( (float) 0.8, (float) 0.3, (float) 0.8));
- colhash.put("YELLOW", new Color( (float) 0.8, (float) 0.8, (float) 0.0));
+ colhash.put("RED", new Color((float) 0.9, (float) 0.2, (float) 0.1));
+ colhash.put("BLUE", new Color((float) 0.5, (float) 0.7, (float) 0.9));
+ colhash.put("GREEN", new Color((float) 0.1, (float) 0.8, (float) 0.1));
+ colhash.put("ORANGE", new Color((float) 0.9, (float) 0.6, (float) 0.3));
+ colhash.put("CYAN", new Color((float) 0.1, (float) 0.7, (float) 0.7));
+ colhash.put("PINK", new Color((float) 0.9, (float) 0.5, (float) 0.5));
+ colhash.put("MAGENTA", new Color((float) 0.8, (float) 0.3, (float) 0.8));
+ colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
}
- public ClustalxColourScheme(Vector seqs, int maxWidth)
+ public ClustalxColourScheme(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
{
- resetClustalX(seqs, maxWidth);
+ alignmentChanged(alignment, hiddenReps);
}
- public void resetClustalX(Vector seqs, int maxWidth)
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
{
+ int maxWidth = alignment.getWidth();
+ List<SequenceI> seqs = alignment.getSequences(hiddenReps);
cons2 = new int[maxWidth][24];
- includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to get the current setting of the includeGaps param.
+ includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
+ // get the current setting of the
+ // includeGaps param.
int start = 0;
// Initialize the array
int j = 0;
char[] seq;
- while (j < seqs.size())
+ for (SequenceI sq : seqs)
{
- seq = ( (SequenceI) seqs.elementAt(j)).getSequence();
+ seq = sq.getSequence();
int end_j = seq.length - 1;
for (i = start; i <= end_j; i++)
{
- if ( (seq.length - 1) < i)
+ if ((seq.length - 1) < i)
{
res = 23;
}
j++;
}
-
+
this.size = seqs.size();
makeColours();
}
colours = new ConsensusColour[11];
Consensus[] tmp8 = new Consensus[1];
- tmp8[0] = conses[30]; //G
- colours[7] = new ConsensusColour( (Color) colhash.get("ORANGE"), tmp8);
+ tmp8[0] = conses[30]; // G
+ colours[7] = new ConsensusColour((Color) colhash.get("ORANGE"), tmp8);
Consensus[] tmp9 = new Consensus[1];
- tmp9[0] = conses[31]; //P
- colours[8] = new ConsensusColour( (Color) colhash.get("YELLOW"), tmp9);
+ tmp9[0] = conses[31]; // P
+ colours[8] = new ConsensusColour((Color) colhash.get("YELLOW"), tmp9);
Consensus[] tmp10 = new Consensus[1];
- tmp10[0] = conses[27]; //C
- colours[9] = new ConsensusColour( (Color) colhash.get("PINK"), tmp8);
+ tmp10[0] = conses[27]; // C
+ colours[9] = new ConsensusColour((Color) colhash.get("PINK"), tmp8);
Consensus[] tmp1 = new Consensus[14];
- tmp1[0] = conses[0]; //%
- tmp1[1] = conses[1]; //#
- tmp1[2] = conses[26]; //A
- tmp1[3] = conses[27]; //C
- tmp1[4] = conses[11]; //F
- tmp1[5] = conses[13]; //H
- tmp1[6] = conses[14]; //I
- tmp1[7] = conses[15]; //L
- tmp1[8] = conses[16]; //M
- tmp1[9] = conses[23]; //V
- tmp1[10] = conses[24]; //W
- tmp1[11] = conses[25]; //Y
- tmp1[12] = conses[18]; //P
- tmp1[13] = conses[19]; //p
- colours[0] = new ConsensusColour( (Color) colhash.get("BLUE"), tmp1);
-
- colours[10] = new ConsensusColour( (Color) colhash.get("CYAN"), tmp1);
+ tmp1[0] = conses[0]; // %
+ tmp1[1] = conses[1]; // #
+ tmp1[2] = conses[26]; // A
+ tmp1[3] = conses[27]; // C
+ tmp1[4] = conses[11]; // F
+ tmp1[5] = conses[13]; // H
+ tmp1[6] = conses[14]; // I
+ tmp1[7] = conses[15]; // L
+ tmp1[8] = conses[16]; // M
+ tmp1[9] = conses[23]; // V
+ tmp1[10] = conses[24]; // W
+ tmp1[11] = conses[25]; // Y
+ tmp1[12] = conses[18]; // P
+ tmp1[13] = conses[19]; // p
+ colours[0] = new ConsensusColour((Color) colhash.get("BLUE"), tmp1);
+
+ colours[10] = new ConsensusColour((Color) colhash.get("CYAN"), tmp1);
Consensus[] tmp2 = new Consensus[5];
- tmp2[0] = conses[8]; //t
- tmp2[1] = conses[21]; //S
- tmp2[2] = conses[22]; //T
- tmp2[3] = conses[0]; //%
- tmp2[4] = conses[1]; //#
- colours[1] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp2);
+ tmp2[0] = conses[8]; // t
+ tmp2[1] = conses[21]; // S
+ tmp2[2] = conses[22]; // T
+ tmp2[3] = conses[0]; // %
+ tmp2[4] = conses[1]; // #
+ colours[1] = new ConsensusColour((Color) colhash.get("GREEN"), tmp2);
Consensus[] tmp3 = new Consensus[3];
- tmp3[0] = conses[17]; //N
- tmp3[1] = conses[29]; //D
- tmp3[2] = conses[5]; //n
- colours[2] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp3);
+ tmp3[0] = conses[17]; // N
+ tmp3[1] = conses[29]; // D
+ tmp3[2] = conses[5]; // n
+ colours[2] = new ConsensusColour((Color) colhash.get("GREEN"), tmp3);
Consensus[] tmp4 = new Consensus[6];
tmp4[0] = conses[6]; // q = QE
- tmp4[1] = conses[19]; //Q
- tmp4[2] = conses[22]; //E
- tmp4[3] = conses[3]; //+
- tmp4[4] = conses[28]; //K
- tmp4[5] = conses[20]; //R
- colours[3] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp4);
+ tmp4[1] = conses[19]; // Q
+ tmp4[2] = conses[22]; // E
+ tmp4[3] = conses[3]; // +
+ tmp4[4] = conses[28]; // K
+ tmp4[5] = conses[20]; // R
+ colours[3] = new ConsensusColour((Color) colhash.get("GREEN"), tmp4);
Consensus[] tmp5 = new Consensus[4];
- tmp5[0] = conses[3]; //+
- tmp5[1] = conses[28]; //K
- tmp5[2] = conses[20]; //R
- tmp5[3] = conses[19]; //Q
- colours[4] = new ConsensusColour( (Color) colhash.get("RED"), tmp5);
-
- Consensus[] tmp6 = new Consensus[5];
- tmp6[0] = conses[3]; //-
- tmp6[1] = conses[29]; //D
- tmp6[2] = conses[10]; //E
- tmp6[3] = conses[6]; //q
- tmp6[4] = conses[19]; //Q
- colours[5] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp6);
+ tmp5[0] = conses[3]; // +
+ tmp5[1] = conses[28]; // K
+ tmp5[2] = conses[20]; // R
+ tmp5[3] = conses[19]; // Q
+ colours[4] = new ConsensusColour((Color) colhash.get("RED"), tmp5);
+
+ Consensus[] tmp6 = new Consensus[6];
+ tmp6[0] = conses[3]; // -
+ tmp6[1] = conses[29]; // D
+ tmp6[2] = conses[10]; // E
+ tmp6[3] = conses[6]; // QE
+ tmp6[4] = conses[19]; // Q
+ tmp6[5] = conses[2]; // DE
+ colours[5] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp6);
Consensus[] tmp7 = new Consensus[5];
- tmp7[0] = conses[3]; //-
- tmp7[1] = conses[29]; //D
- tmp7[2] = conses[10]; //E
- tmp7[3] = conses[17]; //N
- tmp7[4] = conses[2]; //DE
- colours[6] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp7);
+ tmp7[0] = conses[3]; // -
+ tmp7[1] = conses[29]; // D
+ tmp7[2] = conses[10]; // E
+ tmp7[3] = conses[17]; // N
+ tmp7[4] = conses[2]; // DE
+ colours[6] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp7);
// Now attach the ConsensusColours to the residue letters
ResidueColour = new ConsensusColour[20];
ResidueColour[19] = colours[0]; // V
}
+ @Override
public Color findColour(char c)
{
return Color.pink;
}
- public Color findColour(char c, int j)
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour;
- if (cons2.length <= j || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
+ if (cons2.length <= j
+ || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
{
return Color.white;
}
for (int k = 0; k < ResidueColour[i].conses.length; k++)
{
- if (ResidueColour[i].conses[k].isConserved(cons2, j, size, includeGaps))
+ if (ResidueColour[i].conses[k].isConserved(cons2, j, size,
+ includeGaps))
{
currentColour = ResidueColour[i].c;
}
}
/**
- * @param includeGaps the includeGaps to set
+ * @param includeGaps
+ * the includeGaps to set
*/
protected void setIncludeGaps(boolean includeGaps)
{
this.includeGaps = includeGaps;
}
+
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ ClustalxColourScheme css = new ClustalxColourScheme(sg,
+ hiddenRepSequences);
+ css.includeGaps = includeGaps;
+ return css;
+ }
}
class ConsensusColour
{
Consensus[] conses;
+
Color c;
public ConsensusColour(Color c, Consensus[] conses)
{
this.conses = conses;
- // this.list = list;
+ // this.list = list;
this.c = c;
}
}
git://source.jalview.org / jalview.git / blobdiff