diff --git a/uk/ac/sanger/artemis/AlignMatchVector.java b/uk/ac/sanger/artemis/AlignMatchVector.java
index 86dc47437da6e449f950a51f81082a4e6a50edc0..646e82e9853c5438ddd1af8e209ed7208f70f864 100644
--- a/uk/ac/sanger/artemis/AlignMatchVector.java
+++ b/uk/ac/sanger/artemis/AlignMatchVector.java
@@ -3,19 +3,19 @@
* created: Sat Jun 17 2000
*
* This file is part of Artemis
- *
+ *
* Copyright (C) 2000,2001 Genome Research Limited
- *
+ *
* This program 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 2
* of the License, or (at your option) any later version.
- *
+ *
* This program 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 this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -51,7 +51,7 @@ public class AlignMatchVector {
public void addElement (AlignMatch item) {
vector.add (item);
}
-
+
/**
* Appends the given AlignMatch object to the vector if and only if it
* isn't already in the vector. (same as addElement ()).
@@ -59,7 +59,7 @@ public class AlignMatchVector {
public void add (AlignMatch item) {
addElement (item);
}
-
+
/**
* Performs the same function as Vector.elementAt ()
**/
@@ -101,13 +101,13 @@ public class AlignMatchVector {
public int size () {
return vector.size ();
}
-
+
/**
* Sort this vector.
* @param cmp The returned vector will be sorted with this Comparator.
**/
public void sort (final Comparator cmp) {
- vector = vector.sort (cmp);
+ vector = vector.mysort (cmp);
}
/**
diff --git a/uk/ac/sanger/artemis/FeatureVector.java b/uk/ac/sanger/artemis/FeatureVector.java
index 4f1c4c6a8feac0fc6e7fd950c0ef4ea96aaec39e..a0623aa9c2c37183191231ab14d0f210c9c86ceb 100644
--- a/uk/ac/sanger/artemis/FeatureVector.java
+++ b/uk/ac/sanger/artemis/FeatureVector.java
@@ -154,7 +154,7 @@ public class FeatureVector {
public FeatureVector sort (final Comparator cmp) {
final FeatureVector return_vector = (FeatureVector) clone ();
- return_vector.vector = return_vector.vector.sort (cmp);
+ return_vector.vector = return_vector.vector.mysort (cmp);
return return_vector;
}
diff --git a/uk/ac/sanger/artemis/io/KeyVector.java b/uk/ac/sanger/artemis/io/KeyVector.java
index 95aa4555ee144967888a735b5f741b4dfcf8d2c8..b5b89937648da923df00b22535cbdb0426afc44c 100644
--- a/uk/ac/sanger/artemis/io/KeyVector.java
+++ b/uk/ac/sanger/artemis/io/KeyVector.java
@@ -3,19 +3,19 @@
* created: Fri Apr 16 1999
*
* This file is part of Artemis
- *
+ *
* Copyright (C) 1999 Genome Research Limited
- *
+ *
* This program 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 2
* of the License, or (at your option) any later version.
- *
+ *
* This program 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 this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -39,13 +39,13 @@ public class KeyVector extends FastVector
public KeyVector ()
{
- super();
+ super();
}
-
+
/**
* Create a new vector which contains only the given Key.
**/
- public KeyVector (final Key new_key)
+ public KeyVector (final Key new_key)
{
super();
add (new_key);
@@ -54,7 +54,7 @@ public class KeyVector extends FastVector
/**
* Return a new copy of this object.
**/
- public KeyVector copy ()
+ public KeyVector copy ()
{
final KeyVector new_key_vector = (KeyVector)clone();
@@ -65,21 +65,21 @@ public class KeyVector extends FastVector
* Sorts the elements of the vector using a simple O(n^2) selection
* sort.
*/
- public void sort()
+ public void mysort()
{
int smallest;
- for (int i = 0; i < size (); ++i)
+ for (int i = 0; i < size (); ++i)
{
//find smallest remaining element
smallest = i;
- for(int j = i + 1 ; j < size () ; ++j)
+ for(int j = i + 1 ; j < size () ; ++j)
{
- if(((Key)get(j)).compareTo( (Key)get(smallest)) < 0)
+ if(((Key)get(j)).compareTo( (Key)get(smallest)) < 0)
smallest = j;
}
//exchange smallest and i
- if (smallest != i)
+ if (smallest != i)
{
final Key tmp = (Key)get(i);
setElementAt (get(smallest), i);
diff --git a/uk/ac/sanger/artemis/io/SimpleEntryInformation.java b/uk/ac/sanger/artemis/io/SimpleEntryInformation.java
index 81cdcb0866aea7ca1c9cd35fb59c94154ee8f038..db4dde0d324ca27b248c3f3063701e9e4dcf7895 100644
--- a/uk/ac/sanger/artemis/io/SimpleEntryInformation.java
+++ b/uk/ac/sanger/artemis/io/SimpleEntryInformation.java
@@ -175,7 +175,7 @@ public class SimpleEntryInformation
return null;
}
- return_vector.sort ();
+ return_vector.mysort ();
return return_vector;
}
@@ -187,11 +187,11 @@ public class SimpleEntryInformation
if (isValidKey (misc_feature_key))
return misc_feature_key;
-
+
misc_feature_key = new Key ("region");
if (isValidKey (misc_feature_key))
return misc_feature_key;
-
+
return (Key)getValidKeys ().get (0);
}
@@ -397,7 +397,7 @@ public class SimpleEntryInformation
return getQualifierInfoHash ().copy ();
}
}
-
+
/**
* Fix this EntryInformation so that the given exception won't happen
* again.
diff --git a/uk/ac/sanger/artemis/util/FastVector.java b/uk/ac/sanger/artemis/util/FastVector.java
index b9d1712f01847e670521acf00c7d91ec0d72b441..d79dc474ab6220c09c862095e3d70c4357a954fe 100644
--- a/uk/ac/sanger/artemis/util/FastVector.java
+++ b/uk/ac/sanger/artemis/util/FastVector.java
@@ -3,19 +3,19 @@
* created: Sun Feb 20 2000
*
* This file is part of Artemis
- *
+ *
* Copyright (C) 2000 Genome Research Limited
- *
+ *
* This program 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 2
* of the License, or (at your option) any later version.
- *
+ *
* This program 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 this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -43,9 +43,9 @@ public class FastVector extends ArrayList
/**
* Performs the same function as Vector.addElement()
*/
- public boolean add(Object object)
+ public boolean add(Object object)
{
- if(object == null)
+ if(object == null)
throw new Error("internal error - adding a null object");
else if(contains(object))
throw new Error("internal error - object added a second time");
@@ -56,24 +56,24 @@ public class FastVector extends ArrayList
/**
* Performs the same function as Vector.lastElement()
**/
- public Object lastElement()
+ public Object lastElement()
{
return (Object)get(size() - 1);
}
-
+
/**
* Insert an Object after another.
* @param old_object The new_object will be inserted after this object
* or at the start if old_object isn't in the vector.
* @param new_object The new object to insert.
**/
- public void insertElementAfter(Object old_object, Object new_object)
+ public void insertElementAfter(Object old_object, Object new_object)
{
final int old_object_index = indexOf(old_object);
- if(old_object_index == -1)
+ if(old_object_index == -1)
add(0, new_object);
- else
+ else
add(old_object_index + 1, new_object);
}
@@ -81,7 +81,7 @@ public class FastVector extends ArrayList
* Replace the Object at the given index. (Performs the same function as
* Vector.elementAt())
**/
- public void setElementAt(final Object object, final int index)
+ public void setElementAt(final Object object, final int index)
{
remove(index);
add(index, object);
@@ -91,7 +91,7 @@ public class FastVector extends ArrayList
* Return a sorted copy of this vector.
* @param cmp The returned vector will be sorted with this Comparator.
**/
- public FastVector sort(final Comparator cmp)
+ public FastVector mysort(final Comparator cmp)
{
final FastVector return_vector = (FastVector)clone();
Collections.sort(return_vector, cmp);
diff --git a/uk/ac/sanger/artemis/util/StringVector.java b/uk/ac/sanger/artemis/util/StringVector.java
index 95f560d579a90ea74c2f1060d6a6e1bb08440016..ce3495b3a9d44a4a12f5d238f9d0673d19a9e762 100644
--- a/uk/ac/sanger/artemis/util/StringVector.java
+++ b/uk/ac/sanger/artemis/util/StringVector.java
@@ -51,11 +51,11 @@ public class StringVector extends Vector<String>
/**
* Create a new vector which contains the given Strings.
**/
- public StringVector(final String[] new_strings)
+ public StringVector(final String[] new_strings)
{
super(new_strings.length);
int len = new_strings.length;
- for(int i = 0; i < len; ++i)
+ for(int i = 0; i < len; ++i)
add(new_strings[i]);
}
@@ -68,7 +68,7 @@ public class StringVector extends Vector<String>
/**
* Create a new vector which contains the given Strings.
**/
- public StringVector(final StringVector new_strings)
+ public StringVector(final StringVector new_strings)
{
super(new_strings);
}
@@ -76,7 +76,7 @@ public class StringVector extends Vector<String>
/**
* Call add() on each of the String objects in the given StringVector.
**/
- public void add(final StringVector new_strings)
+ public void add(final StringVector new_strings)
{
for (int i = 0; i < new_strings.size(); ++i)
add (new_strings.elementAt(i));
@@ -87,19 +87,19 @@ public class StringVector extends Vector<String>
* package.
*/
public void sort()
- {
+ {
final Comparator<String> comparator = new Comparator<String>()
{
- public int compare(String fst, String snd)
+ public int compare(String fst, String snd)
{
- if(fst == null)
+ if(fst == null)
{
if(snd == null)
return 0;
else
return -1;
- }
- else
+ }
+ else
{
if(snd == null)
return 1;
@@ -114,7 +114,7 @@ public class StringVector extends Vector<String>
/**
* Return a new copy of this object.
**/
- public StringVector copy()
+ public StringVector copy()
{
return new StringVector(this);
}
@@ -132,7 +132,7 @@ public class StringVector extends Vector<String>
**/
public static StringVector getStrings(final String argument,
final String delim,
- final boolean keep_zero_char_toks)
+ final boolean keep_zero_char_toks)
{
final StringVector strVector = new StringVector();
@@ -153,23 +153,23 @@ public class StringVector extends Vector<String>
if(idx2 < 0)
idx2 = argLen;
-
+
tok = argument.substring(idx1,idx2);
idx1 = idx2+1;
if(tok.length() == 1 &&
- delim.indexOf(tok.charAt(0)) != -1)
+ delim.indexOf(tok.charAt(0)) != -1)
{
// ignore the split characters
if(keep_zero_char_toks &&
(lastTok == null ||
lastTok != null && lastTok.length () == 1 &&
- delim.indexOf (lastTok) != -1))
+ delim.indexOf (lastTok) != -1))
{
// add a space because of two split_characters in a row
strVector.add("");
}
- }
+ }
else
strVector.add(tok);
@@ -186,7 +186,7 @@ public class StringVector extends Vector<String>
* vector will be zero length.
**/
public static StringVector getStrings(final String argument,
- final String split_characters)
+ final String split_characters)
{
return getStrings(argument, split_characters, false);
}
@@ -198,7 +198,7 @@ public class StringVector extends Vector<String>
* String is zero length or it consists only of whitespace, the return
* vector will be zero length.
**/
- public static StringVector getStrings(final String argument)
+ public static StringVector getStrings(final String argument)
{
return getStrings(argument, " ", false);
}