X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=288d476ff3fc150f54d95bfdfd6b540c332f5d5f;hb=6a495a81e764c82f9fdfb6b3f990b962a5b85286;hp=67d50eea97a7b16035c9272a48c585f2d38b3d05;hpb=1c1cbbbba95796cbd8aeea8db28633eb84aa61a4;p=jalview.git
diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
old mode 100755
new mode 100644
index 67d50ee..288d476
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,27 +1,31 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* 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 Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+
import java.io.File;
import java.io.InputStream;
-import jalview.datamodel.*;
-
/**
* A low level class for alignment and feature IO with alignment formatting
* methods used by both applet and application for generating flat alignment
@@ -37,15 +41,15 @@ public class AppletFormatAdapter
* List of valid format strings used in the isValidFormat method
*/
public static final String[] READABLE_FORMATS = new String[]
- { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
- "PDB", "JnetFile" }; // , "SimpleBLAST" };
-
+ { "BLC", "CLUSTAL", "FASTA", "MEGA", "MSF", "PileUp", "PIR", "PFAM",
+ "PDB", "JnetFile", "RNAML" };
/**
* List of valid format strings for use by callers of the formatSequences
* method
*/
public static final String[] WRITEABLE_FORMATS = new String[]
- { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
+ { "BLC", "CLUSTAL", "FASTA", "MEGA", "MSF", "PileUp", "PIR", "PFAM",
+ "STH",
"AMSA" };
/**
@@ -53,35 +57,33 @@ public class AppletFormatAdapter
* that are writable by the application.
*/
public static final String[] WRITABLE_EXTENSIONS = new String[]
- { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
- "sto,stk" };
+ { "fa, fasta, mfa, fastq", "aln", "pfam", "meg", "msf", "pir", "blc", "amsa",
+ "jvp", "sto,stk", "jar" };
/**
* List of writable formats by the application. Order must correspond with the
* WRITABLE_EXTENSIONS list of formats.
*/
public static final String[] WRITABLE_FNAMES = new String[]
- { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
- "STH" };
+ { "Fasta", "Clustal", "PFAM", "MEGA", "MSF", "PIR", "BLC", "AMSA",
+ "Jalview",
+ "STH", "Jalview"};
/**
* List of readable format file extensions by application in order
* corresponding to READABLE_FNAMES
*/
public static final String[] READABLE_EXTENSIONS = new String[]
- { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
- "sto,stk" }; // ,
-
- // ".blast"
- // };
+ { "fa, fasta, mfa, fastq", "aln", "pfam", "meg", "msf", "pir", "blc", "amsa",
+ "jar,jvp", "sto,stk", "xml,rnaml" }; // ".blast"
/**
* List of readable formats by application in order corresponding to
* READABLE_EXTENSIONS
*/
public static final String[] READABLE_FNAMES = new String[]
- { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
- "Stockholm" };// ,
+ { "Fasta", "Clustal", "PFAM", "MEGA", "MSF", "PIR", "BLC", "AMSA", "Jalview",
+ "Stockholm", "RNAML" };
// "SimpleBLAST"
// };
@@ -231,6 +233,8 @@ public class AppletFormatAdapter
else if (format.equals("PDB"))
{
afile = new MCview.PDBfile(inFile, type);
+ // Uncomment to test Jmol data based PDB processing: JAL-1213
+ // afile = new jalview.ext.jmol.PDBFileWithJmol(inFile, type);
}
else if (format.equals("STH"))
{
@@ -240,6 +244,14 @@ public class AppletFormatAdapter
{
afile = new SimpleBlastFile(inFile, type);
}
+ else if (format.equals("RNAML"))
+ {
+ afile = new RnamlFile(inFile, type);
+ }
+ else if (format.equals("MEGA"))
+ {
+ afile = new MegaFile(inFile, type);
+ }
Alignment al = new Alignment(afile.getSeqsAsArray());
@@ -295,7 +307,7 @@ public class AppletFormatAdapter
*
* @return DOCUMENT ME!
*/
- public Alignment readFromFile(FileParse source, String format)
+ public AlignmentI readFromFile(FileParse source, String format)
throws java.io.IOException
{
// TODO: generalise mapping between format string and io. class instances
@@ -347,10 +359,18 @@ public class AppletFormatAdapter
{
afile = new StockholmFile(source);
}
+ else if (format.equals("RNAML"))
+ {
+ afile = new RnamlFile(source);
+ }
else if (format.equals("SimpleBLAST"))
{
afile = new SimpleBlastFile(source);
}
+ else if (format.equals("MEGA"))
+ {
+ afile = new MegaFile(source);
+ }
Alignment al = new Alignment(afile.getSeqsAsArray());
@@ -454,6 +474,14 @@ public class AppletFormatAdapter
{
afile = new AMSAFile(alignment);
}
+ else if (format.equalsIgnoreCase("RNAML"))
+ {
+ afile = new RnamlFile();
+ }
+ else if (format.equalsIgnoreCase("MEGA"))
+ {
+ afile = new MegaFile();
+ }
else
{
throw new Exception(
@@ -505,47 +533,43 @@ public class AppletFormatAdapter
{
System.out.println("Reading file: " + f);
AppletFormatAdapter afa = new AppletFormatAdapter();
- String fName = f.getName();
+ Runtime r = Runtime.getRuntime();
+ System.gc();
+ long memf = -r.totalMemory() + r.freeMemory();
+ long t1 = -System.currentTimeMillis();
+ Alignment al = afa.readFile(args[i], FILE,
+ new IdentifyFile().Identify(args[i], FILE));
+ t1 += System.currentTimeMillis();
+ System.gc();
+ memf += r.totalMemory() - r.freeMemory();
+ if (al != null)
{
- Runtime r = Runtime.getRuntime();
- System.gc();
- long memf = -r.totalMemory() + r.freeMemory();
- long t1 = -System.currentTimeMillis();
- Alignment al = afa.readFile(args[i], FILE,
- new IdentifyFile().Identify(args[i], FILE));
- t1 += System.currentTimeMillis();
- System.gc();
- memf += r.totalMemory() - r.freeMemory();
- if (al != null)
+ System.out.println("Alignment contains " + al.getHeight()
+ + " sequences and " + al.getWidth() + " columns.");
+ try
{
- System.out.println("Alignment contains " + al.getHeight()
- + " sequences and " + al.getWidth() + " columns.");
- try
- {
- System.out.println(new AppletFormatAdapter()
- .formatSequences("FASTA", al, true));
- } catch (Exception e)
- {
- System.err
- .println("Couln't format the alignment for output as a FASTA file.");
- e.printStackTrace(System.err);
- }
- }
- else
+ System.out.println(new AppletFormatAdapter().formatSequences(
+ "FASTA", al, true));
+ } catch (Exception e)
{
- System.out.println("Couldn't read alignment");
+ System.err
+ .println("Couln't format the alignment for output as a FASTA file.");
+ e.printStackTrace(System.err);
}
- System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
- System.out
- .println("Difference between free memory now and before is "
- + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
}
+ else
+ {
+ System.out.println("Couldn't read alignment");
+ }
+ System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
+ System.out
+ .println("Difference between free memory now and before is "
+ + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
} catch (Exception e)
{
System.err.println("Exception when dealing with " + i
+ "'th argument: " + args[i] + "\n" + e);
}
-
}
else
{
@@ -726,5 +750,4 @@ public class AppletFormatAdapter
}
return null;
}
-
}