/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
int[] seq2;\r
SequenceI s1;\r
SequenceI s2;\r
- String s1str;\r
- String s2str;\r
+ public String s1str;\r
+ public String s2str;\r
int maxi;\r
int maxj;\r
int[] aseq1;\r
int[] aseq2;\r
- String astr1 = "";\r
- String astr2 = "";\r
+ public String astr1="";\r
+ public String astr2="";\r
\r
/** DOCUMENT ME!! */\r
public int seq1start;\r
int[][] lookup = ResidueProperties.getBLOSUM62();\r
String[] intToStr = pep;\r
int defInt = 23;\r
- String output = "";\r
+ StringBuffer output = new StringBuffer();\r
String type;\r
- Runtime rt;\r
-\r
\r
/**\r
* Creates a new AlignSeq object.\r
*/\r
public AlignSeq(SequenceI s1, SequenceI s2, String type)\r
{\r
- rt = Runtime.getRuntime();\r
- SeqInit(s1, s2, type);\r
+ SeqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(), type);\r
+ }\r
+\r
+ /**\r
+ * Creates a new AlignSeq object.\r
+ *\r
+ * @param s1 DOCUMENT ME!\r
+ * @param s2 DOCUMENT ME!\r
+ * @param type DOCUMENT ME!\r
+ */\r
+ public AlignSeq(SequenceI s1,\r
+ String string1,\r
+ SequenceI s2,\r
+ String string2,\r
+ String type)\r
+ {\r
+ SeqInit(s1, string1, s2, string2, type);\r
}\r
\r
/**\r
*/\r
public String getOutput()\r
{\r
- return output;\r
+ return output.toString();\r
}\r
\r
/**\r
* @param s2 DOCUMENT ME!\r
* @param type DOCUMENT ME!\r
*/\r
- public void SeqInit(SequenceI s1, SequenceI s2, String type)\r
+ public void SeqInit(SequenceI s1,\r
+ String string1,\r
+ SequenceI s2,\r
+ String string2,\r
+ String type)\r
{\r
- s1str = extractGaps(jalview.util.Comparison.GapChars, s1.getSequence());\r
- s2str = extractGaps(jalview.util.Comparison.GapChars, s2.getSequence());\r
+\r
+ s1str = extractGaps(jalview.util.Comparison.GapChars, string1);\r
+ s2str = extractGaps(jalview.util.Comparison.GapChars, string2);\r
+\r
+ if(s1str.length()==0 || s2str.length()==0)\r
+ {\r
+ System.out.println("ALL GAPS: " +\r
+ (s1str.length()==0?s1.getName():" ")\r
+ +(s2str.length()==0?s2.getName():""));\r
+ return;\r
+ }\r
\r
this.s1 = s1;\r
this.s2 = s2;\r
}\r
else\r
{\r
- output = output + ("Wrong type = dna or pep only");\r
+ output.append("Wrong type = dna or pep only");\r
System.exit(0);\r
}\r
\r
/**\r
* DOCUMENT ME!\r
*/\r
- public void printAlignment()\r
+ public void printAlignment(java.io.PrintStream os)\r
{\r
// Find the biggest id length for formatting purposes\r
int maxid = s1.getName().length();\r
int nochunks = ((aseq1.length - count) / len) + 1;\r
pid = 0;\r
\r
- output = output + ("Score = " + score[maxi][maxj] + "\n");\r
- output = output +\r
- ("Length of alignment = " + (aseq1.length - count) + "\n");\r
- output = output + ("Sequence ");\r
- output = output + (new Format("%" + maxid + "s").form(s1.getName()));\r
- output = output +\r
- (" : " + seq1start + " - " + seq1end + " (Sequence length = " +\r
+ output.append("Score = " + score[maxi][maxj] + "\n");\r
+ output.append("Length of alignment = " + (aseq1.length - count) + "\n");\r
+ output.append("Sequence ");\r
+ output.append(new Format("%" + maxid + "s").form(s1.getName()));\r
+ output.append(" : " + s1.getStart() + " - " + s1.getEnd() + " (Sequence length = " +\r
s1str.length() + ")\n");\r
- output = output + ("Sequence ");\r
- output = output + (new Format("%" + maxid + "s").form(s2.getName()));\r
- output = output +\r
- (" : " + seq2start + " - " + seq2end + " (Sequence length = " +\r
+ output .append("Sequence ");\r
+ output.append(new Format("%" + maxid + "s").form(s2.getName()));\r
+ output.append(" : " + s2.getStart() + " - " + s2.getEnd() + " (Sequence length = " +\r
s2str.length() + ")\n\n");\r
\r
for (int j = 0; j < nochunks; j++)\r
{\r
// Print the first aligned sequence\r
- output = output +\r
- (new Format("%" + (maxid) + "s").form(s1.getName()) + " ");\r
+ output.append(new Format("%" + (maxid) + "s").form(s1.getName()) + " ");\r
\r
for (int i = 0; i < len; i++)\r
{\r
if ((count + i + (j * len)) < aseq1.length)\r
{\r
- output = output +\r
- (new Format("%s").form(intToStr[aseq1[count + i +\r
+ output.append(new Format("%s").form(intToStr[aseq1[count + i +\r
(j * len)]]));\r
}\r
}\r
\r
- output = output + ("\n");\r
- output = output +\r
- (new Format("%" + (maxid) + "s").form(" ") + " ");\r
+ output.append("\n");\r
+ output.append(new Format("%" + (maxid) + "s").form(" ") + " ");\r
\r
// Print out the matching chars\r
for (int i = 0; i < len; i++)\r
!intToStr[aseq1[count + i + (j * len)]].equals("-"))\r
{\r
pid++;\r
- output = output + ("|");\r
+ output.append("|");\r
}\r
else if (type.equals("pep"))\r
{\r
intToStr[aseq1[count + i + (j * len)]],\r
intToStr[aseq2[count + i + (j * len)]]) > 0)\r
{\r
- output = output + (".");\r
+ output.append(".");\r
}\r
else\r
{\r
- output = output + (" ");\r
+ output.append(" ");\r
}\r
}\r
else\r
{\r
- output = output + (" ");\r
+ output.append(" ");\r
}\r
}\r
}\r
\r
// Now print the second aligned sequence\r
- output = output + ("\n");\r
- output = output +\r
- (new Format("%" + (maxid) + "s").form(s2.getName()) + " ");\r
+ output = output.append("\n");\r
+ output = output.append(new Format("%" + (maxid) + "s").form(s2.getName()) + " ");\r
\r
for (int i = 0; i < len; i++)\r
{\r
if ((count + i + (j * len)) < aseq1.length)\r
{\r
- output = output +\r
- (new Format("%s").form(intToStr[aseq2[count + i +\r
+ output .append(new Format("%s").form(intToStr[aseq2[count + i +\r
(j * len)]]));\r
}\r
}\r
\r
- output = output + ("\n\n");\r
+ output = output .append("\n\n");\r
}\r
\r
pid = pid / (float) (aseq1.length - count) * 100;\r
- output = output + (new Format("Percentage ID = %2.2f\n\n").form(pid));\r
+ output = output.append(new Format("Percentage ID = %2.2f\n\n").form(pid));\r
+\r
+ try{\r
+ os.print(output.toString());\r
+ }catch(Exception ex){}\r
}\r
\r
/**\r
public static String extractGaps(String gapChar, String seq)\r
{\r
StringTokenizer str = new StringTokenizer(seq, gapChar);\r
- String newString = "";\r
+ StringBuffer newString = new StringBuffer();\r
\r
while (str.hasMoreTokens())\r
{\r
- newString = newString + str.nextToken();\r
+ newString.append( str.nextToken() );\r
}\r
\r
- return newString;\r
+ return newString.toString();\r
}\r
\r
/**\r
\r
for (int i = 0; i < s.length(); i++)\r
{\r
- String ss = s.substring(i, i + 1).toUpperCase();\r
+ // String ss = s.substring(i, i + 1).toUpperCase();\r
+ char c = s.charAt(i);\r
+ if ('a' <= c && c <= 'z')\r
+ {\r
+ // TO UPPERCASE !!!\r
+ c -= ('a' - 'A');\r
+ }\r
+\r
\r
try\r
{\r
if (type.equals("pep"))\r
{\r
- seq1[i] = ((Integer) ResidueProperties.aaHash.get(ss)).intValue();\r
+ seq1[i] = ResidueProperties.aaIndex[c];\r
}\r
else if (type.equals("dna"))\r
{\r
- seq1[i] = ((Integer) dnaHash.get(ss)).intValue();\r
+ seq1[i] = ResidueProperties.nucleotideIndex[c];\r
}\r
\r
if (seq1[i] > 23)\r
git://source.jalview.org / jalview.git / blobdiff