*/\r
public void parse()\r
{\r
- com.stevesoft.pat.Regex gapre = new com.stevesoft.pat.Regex("\\~",\r
- "-");\r
-\r
int i = 0;\r
boolean seqFlag = false;\r
String key = new String();\r
String head = headers.elementAt(i).toString();\r
String seq = seqhash.get(head).toString();\r
\r
- int start = 1;\r
+ int start = -1;\r
int end = -1;\r
\r
if (maxLength < head.length())\r
\r
\r
// Replace ~ with a sensible gap character\r
- seq = gapre.replaceAll(seq);\r
+ seq = seq.replace('~', '-');\r
\r
Sequence newSeq = new Sequence(head, seq, start, end);\r
\r
*/\r
public static int checkSum(String seq)\r
{\r
- //String chars = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";\r
int check = 0;\r
String sequence = seq.toUpperCase();\r
\r
- String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";\r
- index += "--------------------------------------------------------------------------------------------------------------------------------";\r
-\r
for (int i = 0; i < sequence.length(); i++)\r
{\r
try\r
{\r
- int pos = index.indexOf(sequence.charAt(i));\r
\r
- if (index.charAt(pos)!='_')\r
+ int value = sequence.charAt(i);\r
+ if (value!=-1)\r
{\r
- check += (((i % 57) + 1) * pos);\r
+ check += (i % 57 +1) * value;\r
}\r
}\r
catch (Exception e)\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public static String print(SequenceI[] s, boolean is_NA)\r
+ public static String print(SequenceI[] seqs, boolean is_NA)\r
{\r
- com.stevesoft.pat.Regex re2gap = new com.stevesoft.pat.Regex(\r
- "[" + jalview.util.Comparison.GapChars + "]", "\\~");\r
+\r
+ SequenceI [] s = new SequenceI[seqs.length];\r
\r
StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") +\r
"_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet.\r
int max = 0;\r
int maxid = 0;\r
int i = 0;\r
- String big = "";\r
\r
- while ((i < s.length) && (s[i] != null))\r
+ while ((i < seqs.length) && (seqs[i] != null))\r
{\r
- String sq;\r
- big += (sq = s[i].getSequence());\r
+ // Replace all internal gaps with . and external spaces with ~\r
+ s[i] =new Sequence(seqs[i].getName(),seqs[i].getSequence().replace('-', '.'));\r
+\r
+ StringBuffer sb = new StringBuffer(s[i].getSequence());\r
+ for (int ii = 0; ii < sb.length(); ii++)\r
+ {\r
+ if (sb.charAt(ii) == '.')\r
+ {\r
+ sb.replace(ii, ii + 1, "~");\r
+ }\r
+ else\r
+ break;\r
+ }\r
\r
- if (sq.length() > max)\r
+ for (int ii = sb.length() - 1; ii > 0; ii--)\r
+ {\r
+ if (sb.charAt(ii) == '.')\r
{\r
- max = sq.length();\r
+ sb.replace(ii, ii + 1, "~");\r
+ }\r
+ else\r
+ break;\r
+ }\r
+\r
+ s[i].setSequence(sb.toString());\r
+\r
+ if (s[i].getSequence().length() > max)\r
+ {\r
+ max = s[i].getSequence().length();\r
}\r
\r
i++;\r
"d");\r
i = 0;\r
\r
- long bigcheck = checkSum(big);\r
+ int bigChecksum = 0;\r
+ int [] checksums = new int[s.length];\r
+ while ( i < s.length )\r
+ {\r
+ checksums[i] = checkSum(s[i].getSequence());\r
+ bigChecksum += checksums[i];\r
+ i++;\r
+ }\r
+\r
long maxNB = 0;\r
out.append(" MSF: " + s[0].getSequence().length() + " Type: " +\r
- (is_NA ? "N" : "P") + " Check: " + bigcheck + " ..\n\n\n");\r
+ (is_NA ? "N" : "P") + " Check: " + (bigChecksum%10000) + " ..\n\n\n");\r
\r
String[] nameBlock = new String[s.length];\r
String[] idBlock = new String[s.length];\r
\r
+ i=0;\r
while ((i < s.length) && (s[i] != null))\r
{\r
- String name = s[i].getName() + "/" + s[i].getStart() + "-" +\r
- s[i].getEnd();\r
- int check = checkSum(s[i].getSequence());\r
- nameBlock[i] = new String(" Name: " + name + " ");\r
+ nameBlock[i] = new String(" Name: " + s[i].getName() + " ");\r
idBlock[i] = new String("Len: " +\r
- maxLenpad.form(s[i].getSequence().length()) + " Check:" +\r
- maxChkpad.form(check) + " Weight: 1.00\n");\r
+ maxLenpad.form(s[i].getSequence().length()) + " Check: " +\r
+ maxChkpad.form(checksums[i]) + " Weight: 1.00\n");\r
\r
- if (name.length() > maxid)\r
+ if (s[i].getName().length() > maxid)\r
{\r
- maxid = name.length();\r
+ maxid = s[i].getName().length();\r
}\r
\r
if (nameBlock[i].length() > maxNB)\r
while ((j < s.length) && (s[j] != null))\r
{\r
String name = s[j].getName();\r
- out.append(new Format("%-" + maxid + "s").form(name + "/" +\r
- s[j].getStart() + "-" + s[j].getEnd()) + " ");\r
+ out.append(new Format("%-" + maxid + "s").form(name)+ " ");\r
\r
for (int k = 0; k < 5; k++)\r
{\r
if ((end < s[j].getSequence().length()) &&\r
(start < s[j].getSequence().length()))\r
{\r
- out.append(re2gap.replaceAll(s[j].getSequence()\r
- .substring(start, end)));\r
+ out.append(s[j].getSequence().substring(start, end));\r
\r
if (k < 4)\r
{\r
- // out.append(" ");\r
+ out.append(" ");\r
}\r
else\r
{\r
{\r
if (start < s[j].getSequence().length())\r
{\r
- out.append(re2gap.replaceAll(\r
- s[j].getSequence().substring(start)));\r
+ out.append(s[j].getSequence().substring(start));\r
out.append("\n");\r
}\r
else\r
git://source.jalview.org / jalview.git / blobdiff