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Able to read resources from Zip file
author
amwaterhouse
<Andrew Waterhouse>
Wed, 8 Mar 2006 16:51:44 +0000
(16:51 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Wed, 8 Mar 2006 16:51:44 +0000
(16:51 +0000)
src/jalview/io/AnnotationReader.java
patch
|
blob
|
history
src/jalview/io/AppletFormatAdapter.java
patch
|
blob
|
history
src/jalview/io/FileParse.java
patch
|
blob
|
history
src/jalview/io/IdentifyFile.java
patch
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diff --git
a/src/jalview/io/AnnotationReader.java
b/src/jalview/io/AnnotationReader.java
index
958aa65
..
4325dae
100755
(executable)
--- a/
src/jalview/io/AnnotationReader.java
+++ b/
src/jalview/io/AnnotationReader.java
@@
-13,18
+13,25
@@
public class AnnotationReader
\r
try
\r
{
\r
\r
try
\r
{
\r
-
\r
BufferedReader in = null;
\r
BufferedReader in = null;
\r
- try{
\r
- URL url = new URL(file);
\r
- in = new BufferedReader(new InputStreamReader(url.openStream()));
\r
+ java.io.InputStream is = getClass().getResourceAsStream("/" + file);
\r
+ if (is != null)
\r
+ {
\r
+ in = new BufferedReader(new java.io.InputStreamReader(is));
\r
}
\r
}
\r
- catch(java.net.MalformedURLException ex)
\r
+ else
\r
{
\r
{
\r
- in = new BufferedReader(new FileReader(file));
\r
+ try
\r
+ {
\r
+ URL url = new URL(file);
\r
+ in = new BufferedReader(new InputStreamReader(url.openStream()));
\r
+ }
\r
+ catch (java.net.MalformedURLException ex)
\r
+ {
\r
+ in = new BufferedReader(new FileReader(file));
\r
+ }
\r
}
\r
\r
}
\r
\r
-
\r
String line, label, description, token;
\r
int graphStyle, index;
\r
SequenceI refSeq = null;
\r
String line, label, description, token;
\r
int graphStyle, index;
\r
SequenceI refSeq = null;
\r
diff --git
a/src/jalview/io/AppletFormatAdapter.java
b/src/jalview/io/AppletFormatAdapter.java
index
dca2d0c
..
5f73898
100755
(executable)
--- a/
src/jalview/io/AppletFormatAdapter.java
+++ b/
src/jalview/io/AppletFormatAdapter.java
@@
-50,6
+50,12
@@
formats.addElement("PFAM");
\r
}
\r
\r
formats.addElement("PFAM");
\r
}
\r
\r
+
\r
+ public static String FILE = "File";
\r
+ public static String URL = "URL";
\r
+ public static String PASTE = "Paste";
\r
+ public static String CLASSLOADER = "ClassLoader";
\r
+
\r
AlignFile afile = null;
\r
\r
/**
\r
AlignFile afile = null;
\r
\r
/**
\r
@@
-95,6
+101,7
@@
afile = new PfamFile(inFile, type);
\r
}
\r
\r
afile = new PfamFile(inFile, type);
\r
}
\r
\r
+
\r
return afile.getSeqsAsArray();
\r
}
\r
catch (Exception e)
\r
return afile.getSeqsAsArray();
\r
}
\r
catch (Exception e)
\r
diff --git
a/src/jalview/io/FileParse.java
b/src/jalview/io/FileParse.java
index
af3bbec
..
adc57cd
100755
(executable)
--- a/
src/jalview/io/FileParse.java
+++ b/
src/jalview/io/FileParse.java
@@
-24,8
+24,6
@@
import java.net.*;
public class FileParse
\r
{
\r
public File inFile;
\r
public class FileParse
\r
{
\r
public File inFile;
\r
- public int fileSize;
\r
- public int noLines;
\r
protected String type;
\r
protected BufferedReader dataIn;
\r
\r
protected String type;
\r
protected BufferedReader dataIn;
\r
\r
@@
-38,35
+36,33
@@
public class FileParse
{
\r
this.type = type;
\r
\r
{
\r
this.type = type;
\r
\r
- if (type.equals("File"))
\r
+ if (type.equals(AppletFormatAdapter.FILE))
\r
{
\r
this.inFile = new File(fileStr);
\r
{
\r
this.inFile = new File(fileStr);
\r
- this.fileSize = (int) inFile.length();
\r
-
\r
dataIn = new BufferedReader(new FileReader(fileStr));
\r
}
\r
dataIn = new BufferedReader(new FileReader(fileStr));
\r
}
\r
- else if (type.equals("URL"))
\r
+ else if (type.equals(AppletFormatAdapter.URL))
\r
{
\r
URL url = new URL(fileStr);
\r
{
\r
URL url = new URL(fileStr);
\r
- this.fileSize = 0;
\r
dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
\r
}
\r
dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
\r
}
\r
- else if (type.equals("Paste"))
\r
+ else if (type.equals(AppletFormatAdapter.PASTE))
\r
{
\r
dataIn = new BufferedReader(new StringReader(fileStr));
\r
}
\r
{
\r
dataIn = new BufferedReader(new StringReader(fileStr));
\r
}
\r
+ else if (type.equals(AppletFormatAdapter.CLASSLOADER))
\r
+ {
\r
+ java.io.InputStream is = getClass().getResourceAsStream("/" + fileStr);
\r
+ if (is != null)
\r
+ {
\r
+ dataIn = new BufferedReader(new java.io.InputStreamReader(is));
\r
+ }
\r
+ }
\r
}
\r
\r
public String nextLine()
\r
throws IOException
\r
{
\r
}
\r
\r
public String nextLine()
\r
throws IOException
\r
{
\r
- String next = dataIn.readLine();
\r
-
\r
- if (next != null)
\r
- {
\r
- noLines++;
\r
- }
\r
-
\r
- return next;
\r
+ return dataIn.readLine();
\r
}
\r
}
\r
}
\r
}
\r
diff --git
a/src/jalview/io/IdentifyFile.java
b/src/jalview/io/IdentifyFile.java
index
f4beccb
..
2040769
100755
(executable)
--- a/
src/jalview/io/IdentifyFile.java
+++ b/
src/jalview/io/IdentifyFile.java
@@
-39,30
+39,35
@@
public class IdentifyFile
*
\r
* @return DOCUMENT ME!
\r
*/
\r
*
\r
* @return DOCUMENT ME!
\r
*/
\r
- public static String Identify(String file, String protocol)
\r
+ public String Identify(String file, String protocol)
\r
{
\r
String reply = "PFAM";
\r
String error = "FILE NOT FOUND";
\r
{
\r
String reply = "PFAM";
\r
String error = "FILE NOT FOUND";
\r
-
\r
try
\r
{
\r
BufferedReader reader = null;
\r
\r
try
\r
{
\r
BufferedReader reader = null;
\r
\r
- if (protocol.equalsIgnoreCase("File"))
\r
+ if (protocol.equals(AppletFormatAdapter.FILE))
\r
{
\r
{
\r
- reader = new BufferedReader(new FileReader(file));
\r
+ reader = new BufferedReader(new FileReader(file));
\r
}
\r
}
\r
- else if (protocol.equalsIgnoreCase("URL"))
\r
+ else if (protocol.equals(AppletFormatAdapter.URL))
\r
{
\r
{
\r
- error = "URL NOT FOUND";
\r
- URL url = new URL(file);
\r
- reader = new BufferedReader(new InputStreamReader(
\r
- url.openStream()));
\r
+ error = "URL NOT FOUND";
\r
+ URL url = new URL(file);
\r
+ reader = new BufferedReader(new InputStreamReader(
\r
+ url.openStream()));
\r
\r
}
\r
\r
}
\r
- else if (protocol.equalsIgnoreCase("Paste"))
\r
+ else if (protocol.equals(AppletFormatAdapter.PASTE))
\r
+ {
\r
+ reader = new BufferedReader(new StringReader(file));
\r
+ }
\r
+ else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
\r
{
\r
{
\r
- reader = new BufferedReader(new StringReader(file));
\r
+ java.io.InputStream is = getClass().getResourceAsStream("/" +
\r
+ file);
\r
+ reader = new BufferedReader(new java.io.InputStreamReader(is));
\r
}
\r
\r
String data;
\r
}
\r
\r
String data;
\r