*/
package jalview.analysis;
-import java.awt.Color;
-import java.awt.Graphics;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.StringTokenizer;
-
+import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.analysis.scoremodels.ScoreModels;
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;
import jalview.util.MessageManager;
+import java.awt.Color;
+import java.awt.Graphics;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.StringTokenizer;
+
/**
*
*
private static final String NEWLINE = System.lineSeparator();
- static String[] dna =
- { "A", "C", "G", "T", "-" };
+ static String[] dna = { "A", "C", "G", "T", "-" };
// "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", "-" };
+ 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", "-" };
- int[][] score;
+ float[][] score;
- int[][] E;
+ float[][] 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();
+ float[][] lookup = ResidueProperties.getBLOSUM62();
String[] intToStr = pep;
*
* @return DOCUMENT ME!
*/
- public int getMaxScore()
+ public float getMaxScore()
{
return maxscore;
}
seq2 = new int[s2str.length()];
// System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory());
- score = new int[s1str.length()][s2str.length()];
+ score = new float[s1str.length()][s2str.length()];
// System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory());
- E = new int[s1str.length()][s2str.length()];
+ E = new float[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());
if (type.equals(AlignSeq.PEP))
{
- lookup = ResidueProperties.getDefaultPeptideMatrix();
+ lookup = ScoreModels.getInstance().getDefaultModel(true).getMatrix();
}
else if (type.equals(AlignSeq.DNA))
{
- lookup = ResidueProperties.getDefaultDnaMatrix();
+ lookup = ScoreModels.getInstance().getDefaultModel(false).getMatrix();
}
}
else
{
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[] { type2 }));
}
}
public void traceAlignment()
{
// Find the maximum score along the rhs or bottom row
- int max = -9999;
+ float max = -9999;
for (int i = 0; i < seq1.length; i++)
{
}
}
int len = 72 - maxid - 1;
- int nochunks = ((aseq1.length - count) / len) + 1;
+ int nochunks = ((aseq1.length - count) / len)
+ + ((aseq1.length - count) % len > 0 ? 1 : 0);
pid = 0;
output.append("Score = ").append(score[maxi][maxj]).append(NEWLINE);
{
if ((i + (j * len)) < astr1.length())
{
- if (astr1.charAt(i + (j * len)) == astr2.charAt(i + (j * len))
+ 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))))
{
}
pid = pid / (aseq1.length - count) * 100;
- output = output.append(new Format("Percentage ID = %2.2f\n\n")
- .form(pid));
-
+ output = output.append(new Format("Percentage ID = %2.2f\n").form(pid));
try
{
os.print(output.toString());
public int findTrace(int i, int j)
{
int t = 0;
- int max = score[i - 1][j - 1] + (lookup[seq1[i]][seq2[j]] * 10);
+ float max = score[i - 1][j - 1] + (lookup[seq1[i]][seq2[j]] * 10);
if (F[i][j] > max)
{
/**
* 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)
+ public 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)
+ public float max(float f1, float f2)
{
- int max = i1;
+ float max = f1;
- if (i2 > i1)
+ if (f2 > f1)
{
- max = i2;
+ max = f2;
}
return max;
public static void displayMatrix(Graphics g, int[][] mat, int n, int m,
int psize)
{
+ // TODO method dosen't seem to be referenced anywhere delete??
int max = -1000;
int min = 1000;
*/
public static List<List<? extends Object>> replaceMatchingSeqsWith(
List<SequenceI> seqs, List<AlignmentAnnotation> annotations,
- List<SequenceI> ochains,
- AlignmentI al, String dnaOrProtein, boolean removeOldAnnots)
+ List<SequenceI> ochains, AlignmentI al, String dnaOrProtein,
+ boolean removeOldAnnots)
{
List<SequenceI> orig = new ArrayList<SequenceI>(), repl = new ArrayList<SequenceI>();
List<AlignSeq> aligs = new ArrayList<AlignSeq>();
{
ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
ArrayList<AlignSeq> aligns = new ArrayList<AlignSeq>();
-
+
for (SequenceI sq : ochains)
{
SequenceI bestm = null;
AlignSeq bestaseq = null;
- int bestscore = 0;
+ float bestscore = 0;
for (SequenceI msq : al.getSequences())
{
- AlignSeq aseq = doGlobalNWAlignment(msq, sq,
- dnaOrProtein);
+ AlignSeq aseq = doGlobalNWAlignment(msq, sq, dnaOrProtein);
if (bestm == null || aseq.getMaxScore() > bestscore)
{
bestscore = aseq.getMaxScore();
sq.setName(sp.getName());
sq.setDescription(sp.getDescription());
Mapping sp2sq;
- sq.transferAnnotation(sp, sp2sq = aligns.get(q).getMappingFromS1(false));
+ sq.transferAnnotation(sp,
+ sp2sq = aligns.get(q).getMappingFromS1(false));
aligs.add(aligns.get(q));
int inspos = -1;
for (int ap = 0; ap < annotations.size();)
{
inspos = ap;
}
- if (removeOldAnnots) {
+ if (removeOldAnnots)
+ {
annotations.remove(ap);
- } else {
+ }
+ else
+ {
AlignmentAnnotation alan = annotations.remove(ap);
alan.liftOver(sq, sp2sq);
alan.setSequenceRef(sq);
git://source.jalview.org / jalview.git / blobdiff