X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=8f5144b82513b869295806f9a0d4c49563793874;hb=ad1a8c2675db1bda53a09c8acc1c560af9bc8619;hp=47583f0b57fb3b176a5be1d0abcd986fccec3c20;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 47583f0..8f5144b 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,25 +1,40 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 java.io.*;
-import java.net.*;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignViewportI;
+import jalview.util.MessageManager;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+import java.net.MalformedURLException;
+import java.net.URL;
import java.util.zip.GZIPInputStream;
/**
@@ -35,10 +50,26 @@ public class FileParse
public File inFile = null;
- public int index = 1; // sequence counter for FileParse object created from
+ /**
+ * a viewport associated with the current file operation. May be null. May
+ * move to different object.
+ */
+ private AlignViewportI viewport;
- // same data source
+ /**
+ * specific settings for exporting data from the current context
+ */
+ private AlignExportSettingI exportSettings;
+ /**
+ * sequence counter for FileParse object created from same data source
+ */
+ public int index = 1;
+
+ /**
+ * separator for extracting specific 'frame' of a datasource for formats that
+ * support multiple records (e.g. BLC, Stockholm, etc)
+ */
protected char suffixSeparator = '#';
/**
@@ -48,7 +79,7 @@ public class FileParse
public void setNewlineString(String nl)
{
- newline = nl;
+ newline = nl;
}
public String getNewlineString()
@@ -92,11 +123,12 @@ public class FileParse
{
if (from == null)
{
- throw new Error(
- "Implementation error. Null FileParse in copy constructor");
+ throw new Error(MessageManager.getString("error.implementation_error_null_fileparse"));
}
if (from == this)
+ {
return;
+ }
index = ++from.index;
inFile = from.inFile;
suffixSeparator = from.suffixSeparator;
@@ -154,49 +186,59 @@ public class FileParse
{
warningMessage = "Failed to resolve as a GZ stream ("
+ x.getMessage() + ")";
- x.printStackTrace();
+ // x.printStackTrace();
}
;
}
-
+
dataIn = new BufferedReader(new FileReader(fileStr));
dataName = fileStr;
}
return error;
}
- private BufferedReader tryAsGzipSource(InputStream inputStream) throws Exception
+
+ private BufferedReader tryAsGzipSource(InputStream inputStream)
+ throws Exception
{
- BufferedReader inData = new BufferedReader(new InputStreamReader(new GZIPInputStream(inputStream)));
+ BufferedReader inData = new BufferedReader(new InputStreamReader(
+ new GZIPInputStream(inputStream)));
inData.mark(2048);
inData.read();
inData.reset();
return inData;
}
+
private boolean checkURLSource(String fileStr) throws IOException,
MalformedURLException
{
errormessage = "URL NOT FOUND";
URL url = new URL(fileStr);
//
- // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via Kenny Sabir
- Exception e=null;
- if (fileStr.toLowerCase().endsWith(".gz")) {
- try {
- InputStream inputStream = url.openStream();
- dataIn = tryAsGzipSource(inputStream);
- dataName = fileStr;
- return false;
- } catch (Exception ex) {
- e=ex;
+ // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via
+ // Kenny Sabir
+ Exception e = null;
+ if (fileStr.toLowerCase().endsWith(".gz"))
+ {
+ try
+ {
+ InputStream inputStream = url.openStream();
+ dataIn = tryAsGzipSource(inputStream);
+ dataName = fileStr;
+ return false;
+ } catch (Exception ex)
+ {
+ e = ex;
}
}
- try {
+ try
+ {
dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
- } catch (IOException q) {
- if (e!=null)
+ } catch (IOException q)
+ {
+ if (e != null)
{
- throw new IOException("Failed to resolve GZIP stream", e);
+ throw new IOException(MessageManager.getString("exception.failed_to_resolve_gzip_stream"), e);
}
throw q;
}
@@ -251,14 +293,12 @@ public class FileParse
{
if (checkFileSource(suffixLess))
{
- throw new IOException("Problem opening " + inFile
- + " (also tried " + suffixLess + ") : " + errormessage);
+ throw new IOException(MessageManager.formatMessage("exception.problem_opening_file_also_tried", new String[]{inFile.getName(),suffixLess,errormessage}));
}
}
else
{
- throw new IOException("Problem opening " + inFile + " : "
- + errormessage);
+ throw new IOException(MessageManager.formatMessage("exception.problem_opening_file", new String[]{inFile.getName(),errormessage}));
}
}
}
@@ -270,7 +310,9 @@ public class FileParse
{
checkURLSource(fileStr);
if (suffixSeparator == '#')
+ {
extractSuffix(fileStr); // URL lref is stored for later reference.
+ }
} catch (IOException e)
{
String suffixLess = extractSuffix(fileStr);
@@ -312,7 +354,9 @@ public class FileParse
{
String suffixLess = extractSuffix(fileStr);
if (suffixLess != null)
+ {
is = getClass().getResourceAsStream("/" + suffixLess);
+ }
}
if (is != null)
{
@@ -333,8 +377,7 @@ public class FileParse
if (dataIn == null || error)
{
// pass up the reason why we have no source to read from
- throw new IOException("Failed to read data from source:\n"
- + errormessage);
+ throw new IOException(MessageManager.formatMessage("exception.failed_to_read_data_from_source", new String[]{errormessage}));
}
error = false;
dataIn.mark(READAHEAD_LIMIT);
@@ -354,15 +397,17 @@ public class FileParse
}
else
{
- throw new IOException("Unitialised Source Stream");
+ throw new IOException(MessageManager.getString("exception.no_init_source_stream"));
}
}
public String nextLine() throws IOException
{
if (!error)
+ {
return dataIn.readLine();
- throw new IOException("Invalid Source Stream:" + errormessage);
+ }
+ throw new IOException(MessageManager.formatMessage("exception.invalid_source_stream", new String[]{errormessage}));
}
public boolean isValid()
@@ -394,8 +439,7 @@ public class FileParse
}
else
{
- throw new IOException(
- "Implementation Error: Reset called for invalid source.");
+ throw new IOException(MessageManager.getString("error.implementation_error_reset_called_for_invalid_source"));
}
}
@@ -462,4 +506,33 @@ public class FileParse
}
return null;
}
+
+ public AlignViewportI getViewport()
+ {
+ return viewport;
+ }
+
+ public void setViewport(AlignViewportI viewport)
+ {
+ this.viewport = viewport;
+ }
+
+ /**
+ * @return the currently configured exportSettings for writing data.
+ */
+ public AlignExportSettingI getExportSettings()
+ {
+ return exportSettings;
+ }
+
+ /**
+ * Set configuration for export of data.
+ *
+ * @param exportSettings
+ * the exportSettings to set
+ */
+ public void setExportSettings(AlignExportSettingI exportSettings)
+ {
+ this.exportSettings = exportSettings;
+ }
}