*/
package jalview.analysis;
+ import jalview.analysis.scoremodels.PIDModel;
+ import jalview.analysis.scoremodels.ScoreMatrix;
+ import jalview.analysis.scoremodels.ScoreModels;
+ import jalview.analysis.scoremodels.SimilarityParams;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
- import jalview.schemes.ResidueProperties;
- import jalview.schemes.ScoreMatrix;
import jalview.util.Comparison;
import jalview.util.Format;
import jalview.util.MapList;
private static final String NEWLINE = System.lineSeparator();
- static String[] dna = { "A", "C", "G", "T", "-" };
+ float[][] score;
- // "C", "T", "A", "G", "-"};
- static String[] pep = { "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I",
- "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-" };
+ float[][] E;
- int[][] score;
-
- int[][] E;
-
- int[][] F;
+ float[][] F;
int[][] traceback;
int count;
/** DOCUMENT ME!! */
- public int maxscore;
+ public float maxscore;
float pid;
int gapExtend = 20;
- int[][] lookup = ResidueProperties.getBLOSUM62();
-
- String[] intToStr = pep;
-
- int defInt = 23;
-
StringBuffer output = new StringBuffer();
- String type;
+ String type; // AlignSeq.PEP or AlignSeq.DNA
+
+ private ScoreMatrix scoreMatrix;
- private int[] charToInt;
+ private static final int GAP_INDEX = -1;
/**
* Creates a new AlignSeq object.
*
* @param s1
- * DOCUMENT ME!
+ * first sequence for alignment
* @param s2
- * DOCUMENT ME!
+ * second sequence for alignment
* @param type
- * DOCUMENT ME!
+ * molecule type, either AlignSeq.PEP or AlignSeq.DNA
*/
public AlignSeq(SequenceI s1, SequenceI s2, String type)
{
- SeqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(),
+ seqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(),
type);
}
public AlignSeq(SequenceI s1, String string1, SequenceI s2,
String string2, String type)
{
- SeqInit(s1, string1.toUpperCase(), s2, string2.toUpperCase(), type);
+ seqInit(s1, string1.toUpperCase(), s2, string2.toUpperCase(), type);
}
/**
*
* @return DOCUMENT ME!
*/
- public int getMaxScore()
+ public float getMaxScore()
{
return maxscore;
}
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceI getS1()
- {
- return s1;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceI getS2()
- {
- return s2;
- }
-
- /**
*
* @return aligned instance of Seq 1
*/
SequenceI alSeq1 = new Sequence(s1.getName(), getAStr1());
alSeq1.setStart(s1.getStart() + getSeq1Start() - 1);
alSeq1.setEnd(s1.getStart() + getSeq1End() - 1);
- alSeq1.setDatasetSequence(s1.getDatasetSequence() == null ? s1 : s1
- .getDatasetSequence());
+ alSeq1.setDatasetSequence(
+ s1.getDatasetSequence() == null ? s1 : s1.getDatasetSequence());
return alSeq1;
}
SequenceI alSeq2 = new Sequence(s2.getName(), getAStr2());
alSeq2.setStart(s2.getStart() + getSeq2Start() - 1);
alSeq2.setEnd(s2.getStart() + getSeq2End() - 1);
- alSeq2.setDatasetSequence(s2.getDatasetSequence() == null ? s2 : s2
- .getDatasetSequence());
+ alSeq2.setDatasetSequence(
+ s2.getDatasetSequence() == null ? s2 : s2.getDatasetSequence());
return alSeq2;
}
* @param type
* DNA or PEPTIDE
*/
- public void SeqInit(SequenceI s1, String string1, SequenceI s2,
+ public void seqInit(SequenceI s1, String string1, SequenceI s2,
String string2, String type)
{
this.s1 = s1;
this.s2 = s2;
setDefaultParams(type);
- SeqInit(string1, string2);
- }
-
- /**
- * Construct score matrix for sequences with custom substitution matrix
- *
- * @param s1
- * - sequence 1
- * @param string1
- * - string to use for s1
- * @param s2
- * - sequence 2
- * @param string2
- * - string to use for s2
- * @param scoreMatrix
- * - substitution matrix to use for alignment
- */
- public void SeqInit(SequenceI s1, String string1, SequenceI s2,
- String string2, ScoreMatrix scoreMatrix)
- {
- this.s1 = s1;
- this.s2 = s2;
- setType(scoreMatrix.isDNA() ? AlignSeq.DNA : AlignSeq.PEP);
- lookup = scoreMatrix.getMatrix();
+ seqInit(string1, string2);
}
/**
* @param string1
* @param string2
*/
- private void SeqInit(String string1, String string2)
+ private void seqInit(String string1, String string2)
{
s1str = extractGaps(jalview.util.Comparison.GapChars, string1);
s2str = extractGaps(jalview.util.Comparison.GapChars, string2);
if (s1str.length() == 0 || s2str.length() == 0)
{
- output.append("ALL GAPS: "
- + (s1str.length() == 0 ? s1.getName() : " ")
- + (s2str.length() == 0 ? s2.getName() : ""));
+ output.append(
+ "ALL GAPS: " + (s1str.length() == 0 ? s1.getName() : " ")
+ + (s2str.length() == 0 ? s2.getName() : ""));
return;
}
- // System.out.println("lookuip " + rt.freeMemory() + " "+ rt.totalMemory());
- seq1 = new int[s1str.length()];
-
- // System.out.println("seq1 " + rt.freeMemory() +" " + rt.totalMemory());
- seq2 = new int[s2str.length()];
+ score = new float[s1str.length()][s2str.length()];
- // System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory());
- score = new int[s1str.length()][s2str.length()];
+ E = new float[s1str.length()][s2str.length()];
- // System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory());
- E = new int[s1str.length()][s2str.length()];
-
- // System.out.println("E " + rt.freeMemory() + " " + rt.totalMemory());
- F = new int[s1str.length()][s2str.length()];
+ F = new float[s1str.length()][s2str.length()];
traceback = new int[s1str.length()][s2str.length()];
- // System.out.println("F " + rt.freeMemory() + " " + rt.totalMemory());
- seq1 = stringToInt(s1str, type);
-
- // System.out.println("seq1 " + rt.freeMemory() + " " + rt.totalMemory());
- seq2 = stringToInt(s2str, type);
-
- // System.out.println("Seq2 " + rt.freeMemory() + " " + rt.totalMemory());
- // long tstart = System.currentTimeMillis();
- // calcScoreMatrix();
- // long tend = System.currentTimeMillis();
- // System.out.println("Time take to calculate score matrix = " +
- // (tend-tstart) + " ms");
- // printScoreMatrix(score);
- // System.out.println();
- // printScoreMatrix(traceback);
- // System.out.println();
- // printScoreMatrix(E);
- // System.out.println();
- // /printScoreMatrix(F);
- // System.out.println();
- // tstart = System.currentTimeMillis();
- // traceAlignment();
- // tend = System.currentTimeMillis();
- // System.out.println("Time take to traceback alignment = " + (tend-tstart)
- // + " ms");
- }
-
- private void setDefaultParams(String type)
- {
- setType(type);
+ seq1 = indexEncode(s1str);
- if (type.equals(AlignSeq.PEP))
- {
- lookup = ResidueProperties.getDefaultPeptideMatrix();
- }
- else if (type.equals(AlignSeq.DNA))
- {
- lookup = ResidueProperties.getDefaultDnaMatrix();
- }
+ seq2 = indexEncode(s2str);
}
- private void setType(String type2)
+ private void setDefaultParams(String moleculeType)
{
- this.type = type2;
- if (type.equals(AlignSeq.PEP))
- {
- intToStr = pep;
- charToInt = ResidueProperties.aaIndex;
- defInt = ResidueProperties.maxProteinIndex;
- }
- else if (type.equals(AlignSeq.DNA))
- {
- intToStr = dna;
- charToInt = ResidueProperties.nucleotideIndex;
- defInt = ResidueProperties.maxNucleotideIndex;
- }
- else
+ if (!PEP.equals(moleculeType) && !DNA.equals(moleculeType))
{
output.append("Wrong type = dna or pep only");
- throw new Error(MessageManager.formatMessage(
- "error.unknown_type_dna_or_pep", new String[] { type2 }));
+ throw new Error(MessageManager
+ .formatMessage("error.unknown_type_dna_or_pep", new String[]
+ { moleculeType }));
}
+
+ type = moleculeType;
+ scoreMatrix = ScoreModels.getInstance()
+ .getDefaultModel(PEP.equals(type));
}
/**
public void traceAlignment()
{
// Find the maximum score along the rhs or bottom row
- int max = -9999;
+ float max = -Float.MAX_VALUE;
for (int i = 0; i < seq1.length; i++)
{
aseq1 = new int[seq1.length + seq2.length];
aseq2 = new int[seq1.length + seq2.length];
+ StringBuilder sb1 = new StringBuilder(aseq1.length);
+ StringBuilder sb2 = new StringBuilder(aseq2.length);
+
count = (seq1.length + seq2.length) - 1;
- while ((i > 0) && (j > 0))
+ while (i > 0 && j > 0)
{
- if ((aseq1[count] != defInt) && (i >= 0))
- {
- aseq1[count] = seq1[i];
- astr1 = s1str.charAt(i) + astr1;
- }
-
- if ((aseq2[count] != defInt) && (j > 0))
- {
- aseq2[count] = seq2[j];
- astr2 = s2str.charAt(j) + astr2;
- }
+ aseq1[count] = seq1[i];
+ sb1.append(s1str.charAt(i));
+ aseq2[count] = seq2[j];
+ sb2.append(s2str.charAt(j));
trace = findTrace(i, j);
else if (trace == 1)
{
j--;
- aseq1[count] = defInt;
- astr1 = "-" + astr1.substring(1);
+ aseq1[count] = GAP_INDEX;
+ sb1.replace(sb1.length() - 1, sb1.length(), "-");
}
else if (trace == -1)
{
i--;
- aseq2[count] = defInt;
- astr2 = "-" + astr2.substring(1);
+ aseq2[count] = GAP_INDEX;
+ sb2.replace(sb2.length() - 1, sb2.length(), "-");
}
count--;
seq1start = i + 1;
seq2start = j + 1;
- if (aseq1[count] != defInt)
+ if (aseq1[count] != GAP_INDEX)
{
aseq1[count] = seq1[i];
- astr1 = s1str.charAt(i) + astr1;
+ sb1.append(s1str.charAt(i));
}
- if (aseq2[count] != defInt)
+ if (aseq2[count] != GAP_INDEX)
{
aseq2[count] = seq2[j];
- astr2 = s2str.charAt(j) + astr2;
+ sb2.append(s2str.charAt(j));
}
+
+ /*
+ * we built the character strings backwards, so now
+ * reverse them to convert to sequence strings
+ */
+ astr1 = sb1.reverse().toString();
+ astr2 = sb2.reverse().toString();
}
/**
.append(String.valueOf(s2str.length())).append(")")
.append(NEWLINE).append(NEWLINE);
+ ScoreMatrix pam250 = ScoreModels.getInstance().getPam250();
+
for (int j = 0; j < nochunks; j++)
{
// Print the first aligned sequence
output.append(NEWLINE);
output.append(new Format("%" + (maxid) + "s").form(" ")).append(" ");
- // Print out the matching chars
+ /*
+ * Print out the match symbols:
+ * | for exact match (ignoring case)
+ * . if PAM250 score is positive
+ * else a space
+ */
for (int i = 0; i < len; i++)
{
if ((i + (j * len)) < astr1.length())
{
- boolean sameChar = Comparison.isSameResidue(
- astr1.charAt(i + (j * len)), astr2.charAt(i + (j * len)),
- false);
- if (sameChar
- && !jalview.util.Comparison.isGap(astr1.charAt(i
- + (j * len))))
+ char c1 = astr1.charAt(i + (j * len));
+ char c2 = astr2.charAt(i + (j * len));
+ boolean sameChar = Comparison.isSameResidue(c1, c2, false);
+ if (sameChar && !Comparison.isGap(c1))
{
pid++;
output.append("|");
}
else if (type.equals("pep"))
{
- if (ResidueProperties.getPAM250(astr1.charAt(i + (j * len)),
- astr2.charAt(i + (j * len))) > 0)
+ if (pam250.getPairwiseScore(c1, c2) > 0)
{
output.append(".");
}
/**
* DOCUMENT ME!
*
- * @param mat
- * DOCUMENT ME!
- */
- public void printScoreMatrix(int[][] mat)
- {
- int n = seq1.length;
- int m = seq2.length;
-
- for (int i = 0; i < n; i++)
- {
- // Print the top sequence
- if (i == 0)
- {
- Format.print(System.out, "%8s", s2str.substring(0, 1));
-
- for (int jj = 1; jj < m; jj++)
- {
- Format.print(System.out, "%5s", s2str.substring(jj, jj + 1));
- }
-
- System.out.println();
- }
-
- for (int j = 0; j < m; j++)
- {
- if (j == 0)
- {
- Format.print(System.out, "%3s", s1str.substring(i, i + 1));
- }
-
- Format.print(System.out, "%3d ", mat[i][j] / 10);
- }
-
- System.out.println();
- }
- }
-
- /**
- * DOCUMENT ME!
- *
* @param i
* DOCUMENT ME!
* @param j
public int findTrace(int i, int j)
{
int t = 0;
- int max = score[i - 1][j - 1] + (lookup[seq1[i]][seq2[j]] * 10);
+ // float pairwiseScore = lookup[seq1[i]][seq2[j]];
+ float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
+ s2str.charAt(j));
+ float max = score[i - 1][j - 1] + (pairwiseScore * 10);
if (F[i][j] > max)
{
int m = seq2.length;
// top left hand element
- score[0][0] = lookup[seq1[0]][seq2[0]] * 10;
+ score[0][0] = scoreMatrix.getPairwiseScore(s1str.charAt(0),
+ s2str.charAt(0)) * 10;
E[0][0] = -gapExtend;
F[0][0] = 0;
E[0][j] = max(score[0][j - 1] - gapOpen, E[0][j - 1] - gapExtend);
F[0][j] = -gapExtend;
- score[0][j] = max(lookup[seq1[0]][seq2[j]] * 10, -gapOpen, -gapExtend);
+ float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(0),
+ s2str.charAt(j));
+ score[0][j] = max(pairwiseScore * 10, -gapOpen, -gapExtend);
traceback[0][j] = 1;
}
E[i][0] = -gapOpen;
F[i][0] = max(score[i - 1][0] - gapOpen, F[i - 1][0] - gapExtend);
- score[i][0] = max(lookup[seq1[i]][seq2[0]] * 10, E[i][0], F[i][0]);
+ float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
+ s2str.charAt(0));
+ score[i][0] = max(pairwiseScore * 10, E[i][0], F[i][0]);
traceback[i][0] = -1;
}
E[i][j] = max(score[i][j - 1] - gapOpen, E[i][j - 1] - gapExtend);
F[i][j] = max(score[i - 1][j] - gapOpen, F[i - 1][j] - gapExtend);
- score[i][j] = max(score[i - 1][j - 1]
- + (lookup[seq1[i]][seq2[j]] * 10), E[i][j], F[i][j]);
+ float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
+ s2str.charAt(j));
+ score[i][j] = max(score[i - 1][j - 1] + (pairwiseScore * 10),
+ E[i][j], F[i][j]);
traceback[i][j] = findTrace(i, j);
}
}
/**
* DOCUMENT ME!
*
- * @param i1
+ * @param f1
* DOCUMENT ME!
- * @param i2
+ * @param f2
* DOCUMENT ME!
- * @param i3
+ * @param f3
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public int max(int i1, int i2, int i3)
+ private static float max(float f1, float f2, float f3)
{
- int max = i1;
+ float max = f1;
- if (i2 > i1)
+ if (f2 > f1)
{
- max = i2;
+ max = f2;
}
- if (i3 > max)
+ if (f3 > max)
{
- max = i3;
+ max = f3;
}
return max;
/**
* DOCUMENT ME!
*
- * @param i1
+ * @param f1
* DOCUMENT ME!
- * @param i2
+ * @param f2
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public int max(int i1, int i2)
+ private static float max(float f1, float f2)
{
- int max = i1;
+ float max = f1;
- if (i2 > i1)
+ if (f2 > f1)
{
- max = i2;
+ max = f2;
}
return max;
}
/**
- * DOCUMENT ME!
+ * Converts the character string to an array of integers which are the
+ * corresponding indices to the characters in the score matrix
*
* @param s
- * DOCUMENT ME!
- * @param type
- * DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ * @return
*/
- public int[] stringToInt(String s, String type)
+ int[] indexEncode(String s)
{
- int[] seq1 = new int[s.length()];
+ int[] encoded = new int[s.length()];
for (int i = 0; i < s.length(); i++)
{
- // String ss = s.substring(i, i + 1).toUpperCase();
char c = s.charAt(i);
- if ('a' <= c && c <= 'z')
- {
- // TO UPPERCASE !!!
- c -= ('a' - 'A');
- }
-
- try
- {
- seq1[i] = charToInt[c]; // set accordingly from setType
- if (seq1[i] < 0 || seq1[i] > defInt) // set from setType: 23 for
- // peptides, or 4 for NA.
- {
- seq1[i] = defInt;
- }
-
- } catch (Exception e)
- {
- seq1[i] = defInt;
- }
+ encoded[i] = scoreMatrix.getMatrixIndex(c);
}
- return seq1;
+ return encoded;
}
/**
public static void displayMatrix(Graphics g, int[][] mat, int n, int m,
int psize)
{
- // TODO method dosen't seem to be referenced anywhere delete??
+ // TODO method doesn't seem to be referenced anywhere delete??
int max = -1000;
int min = 1000;
*/
public jalview.datamodel.Mapping getMappingFromS1(boolean allowmismatch)
{
- ArrayList<Integer> as1 = new ArrayList<Integer>(), as2 = new ArrayList<Integer>();
+ ArrayList<Integer> as1 = new ArrayList<Integer>(),
+ as2 = new ArrayList<Integer>();
int pdbpos = s2.getStart() + getSeq2Start() - 2;
int alignpos = s1.getStart() + getSeq1Start() - 2;
int lp2 = pdbpos - 3, lp1 = alignpos - 3;
}
// construct range pairs
- int[] mapseq1 = new int[as1.size() + (lastmatch ? 1 : 0)], mapseq2 = new int[as2
- .size() + (lastmatch ? 1 : 0)];
+ int[] mapseq1 = new int[as1.size() + (lastmatch ? 1 : 0)],
+ mapseq2 = new int[as2.size() + (lastmatch ? 1 : 0)];
int i = 0;
for (Integer ip : as1)
{
List<SequenceI> ochains, AlignmentI al, String dnaOrProtein,
boolean removeOldAnnots)
{
- List<SequenceI> orig = new ArrayList<SequenceI>(), repl = new ArrayList<SequenceI>();
+ List<SequenceI> orig = new ArrayList<SequenceI>(),
+ repl = new ArrayList<SequenceI>();
List<AlignSeq> aligs = new ArrayList<AlignSeq>();
if (al != null && al.getHeight() > 0)
{
{
SequenceI bestm = null;
AlignSeq bestaseq = null;
- int bestscore = 0;
+ float bestscore = 0;
for (SequenceI msq : al.getSequences())
{
AlignSeq aseq = doGlobalNWAlignment(msq, sq, dnaOrProtein);
bestm = msq;
}
}
- System.out.println("Best Score for " + (matches.size() + 1) + " :"
- + bestscore);
+ // System.out.println("Best Score for " + (matches.size() + 1) + " :"
+ // + bestscore);
matches.add(bestm);
aligns.add(bestaseq);
al.deleteSequence(bestm);
SequenceI[] originalSequences, String[] omitHidden, int start,
int end, boolean ungapped)
{
+ return (float[]) computeRedundancyMatrixWithRep(originalSequences,
+ omitHidden, start, end, ungapped)[0];
+ }
+
+ public static Object[] computeRedundancyMatrixWithRep(
+ SequenceI[] originalSequences, String[] omitHidden, int start,
+ int end, boolean ungapped)
+ {
+
int height = originalSequences.length;
float[] redundancy = new float[height];
+ SequenceI[] rep = new SequenceI[height];
int[] lngth = new int[height];
for (int i = 0; i < height; i++)
{
// long start = System.currentTimeMillis();
+ SimilarityParams pidParams = new SimilarityParams(true, true, true,
+ true);
float pid;
String seqi, seqj;
for (int i = 0; i < height; i++)
seqj = ug;
}
}
- pid = Comparison.PID(seqi, seqj);
+ pid = (float) PIDModel.computePID(seqi, seqj, pidParams);
// use real sequence length rather than string length
if (lngth[j] < lngth[i])
{
- redundancy[j] = Math.max(pid, redundancy[j]);
+ if (pid > redundancy[j])
+ {
+ rep[j] = originalSequences[i];
+ redundancy[j] = pid;
+ }
}
else
{
- redundancy[i] = Math.max(pid, redundancy[i]);
+ if (pid > redundancy[i])
+ {
+ rep[i] = originalSequences[j];
+ redundancy[i] = pid;
+ }
}
}
}
- return redundancy;
+ return new Object[] { redundancy, rep };
}
}
import jalview.util.MessageManager;
import java.awt.Color;
+import java.util.Arrays;
import java.util.BitSet;
import java.util.List;
SequenceGroup[] gps = null;
if (sg != null && (cs == null || cs.isEmpty()))
{
- gps = jalview.analysis.Grouping.makeGroupsFrom(viewport
- .getSequenceSelection(), viewport.getAlignmentView(true)
- .getSequenceStrings(viewport.getGapCharacter()), viewport
- .getAlignment().getGroups());
+ gps = jalview.analysis.Grouping.makeGroupsFrom(
+ viewport.getSequenceSelection(),
+ viewport.getAlignmentView(true)
+ .getSequenceStrings(viewport.getGapCharacter()),
+ viewport.getAlignment().getGroups());
}
else
{
{
gps = jalview.analysis.Grouping.makeGroupsFromCols(
(sg == null) ? viewport.getAlignment().getSequencesArray()
- : sg.getSequences().toArray(new SequenceI[0]), cs,
- viewport.getAlignment().getGroups());
+ : sg.getSequences().toArray(new SequenceI[0]),
+ cs, viewport.getAlignment().getGroups());
}
}
if (gps != null)
{
- viewport.getAlignment().deleteAllGroups();
- viewport.clearSequenceColours();
- viewport.setSelectionGroup(null);
- // set view properties for each group
- for (int g = 0; g < gps.length; g++)
- {
- // gps[g].setShowunconserved(viewport.getShowUnconserved());
- gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
- viewport.getAlignment().addGroup(gps[g]);
- Color col = new Color((int) (Math.random() * 255),
- (int) (Math.random() * 255), (int) (Math.random() * 255));
- col = col.brighter();
- for (SequenceI sq : gps[g].getSequences(null))
- {
- viewport.setSequenceColour(sq, col);
- }
- }
+ showRandomColoursForGroups(Arrays.asList(gps));
+
return true;
}
return false;
}
@Override
+ public void showRandomColoursForGroups(List<SequenceGroup> gps)
+ {
+ viewport.getAlignment().deleteAllGroups();
+ viewport.clearSequenceColours();
+ viewport.setSelectionGroup(null);
+ // set view properties for each group
+ for (SequenceGroup sg : gps)
+ {
+ // gps[g].setShowunconserved(viewport.getShowUnconserved());
+ sg.setshowSequenceLogo(viewport.isShowSequenceLogo());
+ viewport.getAlignment().addGroup(sg);
+ Color col = new Color((int) (Math.random() * 255),
+ (int) (Math.random() * 255), (int) (Math.random() * 255));
+ col = col.brighter();
+ for (SequenceI sq : sg.getSequences(null))
+ {
+ viewport.setSequenceColour(sq, col);
+ }
+ }
+ }
+
+ @Override
public boolean createGroup()
{
// JBPNote this routine could also mark rows, not just columns.
// need a decent query structure to allow all types of feature searches
BitSet bs = new BitSet();
- SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport
- .getAlignment() : viewport.getSelectionGroup();
+ SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
+ || extendCurrent) ? viewport.getAlignment()
+ : viewport.getSelectionGroup();
int nseq = findColumnsWithFeature(featureType, sqcol, bs);
{
viewport.setColumnSelection(cs);
alignPanel.paintAlignment(true);
- int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
- - bs.cardinality()
+ int columnCount = invert
+ ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+ - bs.cardinality()
: bs.cardinality();
avcg.setStatus(MessageManager.formatMessage(
- "label.view_controller_toggled_marked",
- new String[] {
- toggle ? MessageManager.getString("label.toggled")
- : MessageManager.getString("label.marked"),
+ "label.view_controller_toggled_marked", new String[]
+ { toggle ? MessageManager.getString("label.toggled")
+ : MessageManager.getString("label.marked"),
String.valueOf(columnCount),
invert ? MessageManager
.getString("label.not_containing")
}
else
{
- avcg.setStatus(MessageManager.formatMessage(
- "label.no_feature_of_type_found",
- new String[] { featureType }));
+ avcg.setStatus(MessageManager
+ .formatMessage("label.no_feature_of_type_found", new String[]
+ { featureType }));
if (!extendCurrent)
{
cs.clear();
static int findColumnsWithFeature(String featureType,
SequenceCollectionI sqcol, BitSet bs)
{
- final int startPosition = sqcol.getStartRes() + 1; // converted to base 1
- final int endPosition = sqcol.getEndRes() + 1;
+ final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
+ final int endColumn = sqcol.getEndRes() + 1;
List<SequenceI> seqs = sqcol.getSequences();
int nseq = 0;
for (SequenceI sq : seqs)
{
- boolean sequenceHasFeature = false;
if (sq != null)
{
- SequenceFeature[] sfs = sq.getSequenceFeatures();
- if (sfs != null)
+ // int ist = sq.findPosition(sqcol.getStartRes());
+ List<SequenceFeature> sfs = sq.findFeatures(startColumn,
+ endColumn, featureType);
+
+ if (!sfs.isEmpty())
{
- int ist = sq.findIndex(sq.getStart());
- int iend = sq.findIndex(sq.getEnd());
- if (iend < startPosition || ist > endPosition)
- {
- // sequence not in region
- continue;
- }
- for (SequenceFeature sf : sfs)
+ nseq++;
+ }
+
+ for (SequenceFeature sf : sfs)
+ {
+ int sfStartCol = sq.findIndex(sf.getBegin());
+ int sfEndCol = sq.findIndex(sf.getEnd());
+
+ if (sf.isContactFeature())
{
- // future functionality - featureType == null means mark columns
- // containing all displayed features
- if (sf != null && (featureType.equals(sf.getType())))
+ /*
+ * 'contact' feature - check for 'start' or 'end'
+ * position within the selected region
+ */
+ if (sfStartCol >= startColumn && sfStartCol <= endColumn)
+ {
+ bs.set(sfStartCol - 1);
+ }
+ if (sfEndCol >= startColumn && sfEndCol <= endColumn)
{
- // optimisation - could consider 'spos,apos' like cursor argument
- // - findIndex wastes time by starting from first character and
- // counting
-
- int sfStartCol = sq.findIndex(sf.getBegin());
- int sfEndCol = sq.findIndex(sf.getEnd());
-
- if (sf.isContactFeature())
- {
- /*
- * 'contact' feature - check for 'start' or 'end'
- * position within the selected region
- */
- if (sfStartCol >= startPosition
- && sfStartCol <= endPosition)
- {
- bs.set(sfStartCol - 1);
- sequenceHasFeature = true;
- }
- if (sfEndCol >= startPosition && sfEndCol <= endPosition)
- {
- bs.set(sfEndCol - 1);
- sequenceHasFeature = true;
- }
- continue;
- }
-
- /*
- * contiguous feature - select feature positions (if any)
- * within the selected region
- */
- if (sfStartCol > endPosition || sfEndCol < startPosition)
- {
- // feature is outside selected region
- continue;
- }
- sequenceHasFeature = true;
- if (sfStartCol < startPosition)
- {
- sfStartCol = startPosition;
- }
- if (sfStartCol < ist)
- {
- sfStartCol = ist;
- }
- if (sfEndCol > endPosition)
- {
- sfEndCol = endPosition;
- }
- for (; sfStartCol <= sfEndCol; sfStartCol++)
- {
- bs.set(sfStartCol - 1); // convert to base 0
- }
+ bs.set(sfEndCol - 1);
}
+ continue;
}
- }
- if (sequenceHasFeature)
- {
- nseq++;
+ /*
+ * contiguous feature - select feature positions (if any)
+ * within the selected region
+ */
+ if (sfStartCol < startColumn)
+ {
+ sfStartCol = startColumn;
+ }
+ // not sure what the point of this is
+ // if (sfStartCol < ist)
+ // {
+ // sfStartCol = ist;
+ // }
+ if (sfEndCol > endColumn)
+ {
+ sfEndCol = endColumn;
+ }
+ for (; sfStartCol <= sfEndCol; sfStartCol++)
+ {
+ bs.set(sfStartCol - 1); // convert to base 0
+ }
}
}
}
}
SequenceI[] oldOrder = al.getSequencesArray();
AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
- avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, viewport
- .getAlignment()));
+ avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
boolean featuresFile = false;
try
{
- featuresFile = new FeaturesFile(false, file, protocol).parse(viewport
- .getAlignment().getDataset(), alignPanel.getFeatureRenderer()
- .getFeatureColours(), false, relaxedIdMatching);
+ featuresFile = new FeaturesFile(false, file, protocol).parse(
+ viewport.getAlignment().getDataset(),
+ alignPanel.getFeatureRenderer().getFeatureColours(), false,
+ relaxedIdMatching);
} catch (Exception ex)
{
ex.printStackTrace();
}
// JBPNote this routine could also mark rows, not just columns.
BitSet bs = new BitSet();
- SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport
- .getAlignment() : viewport.getSelectionGroup();
+ SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
+ || extendCurrent) ? viewport.getAlignment()
+ : viewport.getSelectionGroup();
// this could be a lambda... - the remains of the method is boilerplate,
// except for the different messages for reporting selection.
{
viewport.setColumnSelection(cs);
alignPanel.paintAlignment(true);
- int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
- - bs.cardinality()
+ int columnCount = invert
+ ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+ - bs.cardinality()
: bs.cardinality();
avcg.setStatus(MessageManager.formatMessage(
- "label.view_controller_toggled_marked",
- new String[] {
- toggle ? MessageManager.getString("label.toggled")
- : MessageManager.getString("label.marked"),
+ "label.view_controller_toggled_marked", new String[]
+ { toggle ? MessageManager.getString("label.toggled")
+ : MessageManager.getString("label.marked"),
String.valueOf(columnCount),
invert ? MessageManager
.getString("label.not_containing")
import jalview.jbgui.GSliderPanel;
import jalview.util.MessageManager;
+import java.awt.Color;
import java.awt.event.ActionEvent;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
import java.util.Stack;
import java.util.Vector;
Vector redundantSeqs;
+ private SequenceI[] redreps;
+
/**
* Creates a new RedundancyPanel object.
*
}
});
- applyButton.setText(MessageManager.getString("action.remove"));
+ applyButton.setText(MessageManager.getString("action.hide"));
allGroupsCheck.setVisible(false);
slider.setMinimum(0);
slider.setMaximum(100);
frame = new JInternalFrame();
frame.setContentPane(this);
- Desktop.addInternalFrame(frame, MessageManager
- .getString("label.redundancy_threshold_selection"), 400, 100,
- false);
+ Desktop.addInternalFrame(frame,
+ MessageManager
+ .getString("label.redundancy_threshold_selection"),
+ 400, 100, false);
frame.addInternalFrameListener(new InternalFrameAdapter()
{
@Override
{
omitHidden = ap.av.getViewAsString(sg != null);
}
- redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
+ Object rr[] = AlignSeq.computeRedundancyMatrixWithRep(
+ originalSequences,
omitHidden, start, end, false);
+ redundancy = (float[]) rr[0];
+ redreps = (SequenceI[]) rr[1];
+
progress.setIndeterminate(false);
progress.setVisible(false);
progress = null;
- label.setText(MessageManager
- .getString("label.enter_redundancy_threshold"));
+ label.setText(
+ MessageManager.getString("label.enter_redundancy_threshold"));
slider.setVisible(true);
applyButton.setEnabled(true);
valueField.setVisible(true);
@Override
public void applyButton_actionPerformed(ActionEvent e)
{
- Vector del = new Vector();
undoButton.setEnabled(true);
float value = slider.getValue();
SequenceGroup sg = ap.av.getSelectionGroup();
-
+ // delete_seqs(value, sg);
+ hide_seqs(value, sg);
+ }
+ private void hide_seqs(float value, SequenceGroup sg)
+ {
+ /**
+ * hash to look up the representative for a sequence
+ */
+ HashMap<SequenceI, SequenceI> rep = new HashMap<SequenceI, SequenceI>();
+ /**
+ * hash to collect lists of sequences represented by a sequence
+ */
+ HashMap<SequenceI, SequenceGroup> reps = new HashMap<SequenceI, SequenceGroup>();
for (int i = 0; i < redundancy.length; i++)
{
if (value <= redundancy[i])
{
- del.addElement(originalSequences[i]);
+ // does this sequence represent other sequences ?
+ SequenceGroup repset;
+ // is the representative also redundant ?
+ SequenceI repForI = rep.get(redreps[i]);
+ if (repForI==null) {
+ // the representative is still in the alignment.
+ // is it representing anything already ?
+ repset = reps.get(redreps[i]);
+ if (repset==null)
+ {
+ repset = new SequenceGroup();
+ }
+ repset.addSequence(originalSequences[i], false);
+ rep.put(originalSequences[i], redreps[i]);
+ reps.put(redreps[i], repset);
+ // and save the representative sequence for originalSeq
+ repForI = redreps[i];
+ } else {
+ // already hidden the representative for this sequence, so look up its redundant peers
+ repset = reps.get(repForI);
+ if (repset==null)
+ {
+ throw new Error("Implementation failure for redundancy set creation");
+ }
+ // add the sequence to the peerset, and mark sequence's representative in hash
+ repset.addSequence(originalSequences[i], false);
+ rep.put(originalSequences[i], repForI);
+ }
+ // merge any sequences represented by this with its new containing group
+ SequenceGroup existingreps = reps.remove(originalSequences[i]);
+ if (existingreps!=null)
+ {
+ for (SequenceI sq:existingreps.getSequences())
+ {
+ rep.put(sq, repForI);
+ repset.addSequence(sq, false);
+ }
+ }
}
}
+ int s = 0, e = ap.av.getAlignment().getWidth();
+ if (sg != null)
+ {
+ s = sg.getStartRes();
+ e = sg.getEndRes();
+ }
+ List<SequenceGroup> sgs = new ArrayList<SequenceGroup>();
+ for (SequenceI repseq: reps.keySet())
+ {
+ sg = reps.get(repseq);
+ sg.addSequence(repseq, false);
+ sg.setSeqrep(repseq);
+ sg.setStartRes(s);
+ sg.setEndRes(e);
+ sgs.add(sg);
+ }
+ ap.alignFrame.avc.showRandomColoursForGroups(sgs);
+ for (SequenceI repseq : reps.keySet())
+ {
+ sg = reps.get(repseq);
+ ap.av.hideRepSequences(repseq, sg);
+ }
+ }
+
+ private void delete_seqs(float value, SequenceGroup sg)
+ {
+ ArrayList<SequenceI> del = new ArrayList<SequenceI>();
+ for (int i = 0; i < redundancy.length; i++)
+ {
+ if (value <= redundancy[i])
+ {
+ del.add(originalSequences[i]);
+ }
+ }
// This has to be done before the restoreHistoryItem method of alignFrame
// will
// actually restore these sequences.
int width = 0;
for (int i = 0; i < del.size(); i++)
{
- deleted[i] = (SequenceI) del.elementAt(i);
+ deleted[i] = del.get(i);
if (deleted[i].getLength() > width)
{
width = deleted[i].getLength();
ap.alignFrame.addHistoryItem(cut);
PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
{
command.undoCommand(af.getViewAlignments());
ap.av.getHistoryList().remove(command);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
af.updateEditMenuBar();
}
}
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void valueField_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ int i = Integer.parseInt(valueField.getText());
+ slider.setValue(i);
+ } catch (Exception ex)
+ {
+ valueField.setText(slider.getValue() + "");
+ }
+ }
+
}
git://source.jalview.org / jalview.git / commitdiff