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JAL-1894 update year/version in copyright
[jalview.git]
/
src
/
jalview
/
datamodel
/
CigarBase.java
diff --git
a/src/jalview/datamodel/CigarBase.java
b/src/jalview/datamodel/CigarBase.java
index
15c600d
..
420a95e
100644
(file)
--- a/
src/jalview/datamodel/CigarBase.java
+++ b/
src/jalview/datamodel/CigarBase.java
@@
-1,24
+1,28
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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
*
* 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.
*
*
* 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.util.*;
+import jalview.util.MessageManager;
+
+import java.util.Vector;
public abstract class CigarBase
{
public abstract class CigarBase
{
@@
-97,8
+101,7
@@
public abstract class CigarBase
case D:
if (!consecutive_del)
{
case D:
if (!consecutive_del)
{
- deletions[++delcount] = new int[]
- { cursor, 0, alcursor };
+ deletions[++delcount] = new int[] { cursor, 0, alcursor };
}
cursor += range[i];
deletions[delcount][1] = cursor - 1;
}
cursor += range[i];
deletions[delcount][1] = cursor - 1;
@@
-142,7
+145,9
@@
public abstract class CigarBase
endpos = alcursor;
break;
default:
endpos = alcursor;
break;
default:
- throw new Error("Unknown SeqCigar operation '" + operation[i] + "'");
+ throw new Error(MessageManager.formatMessage(
+ "error.unknown_seq_cigar_operation",
+ new String[] { new StringBuffer(operation[i]).toString() }));
}
}
if (++delcount > 0)
}
}
if (++delcount > 0)
@@
-151,9
+156,8
@@
public abstract class CigarBase
System.arraycopy(deletions, 0, trunc_deletions, 0, delcount);
}
deletions = null;
System.arraycopy(deletions, 0, trunc_deletions, 0, delcount);
}
deletions = null;
- return new Object[]
- { ((reference != null) ? sq.toString() : null), new int[]
- { start, startpos, end, endpos }, trunc_deletions };
+ return new Object[] { ((reference != null) ? sq.toString() : null),
+ new int[] { start, startpos, end, endpos }, trunc_deletions };
}
protected void compact_operations()
}
protected void compact_operations()
@@
-221,7
+225,9
@@
public abstract class CigarBase
} while (c >= '0' && c <= '9' && j < l);
if (j >= l && c >= '0' && c <= '9')
{
} while (c >= '0' && c <= '9' && j < l);
if (j >= l && c >= '0' && c <= '9')
{
- throw new Exception("Unterminated cigar string.");
+ throw new Exception(
+ MessageManager
+ .getString("exception.unterminated_cigar_string"));
}
try
{
}
try
{
@@
-230,7
+236,9
@@
public abstract class CigarBase
i = j;
} catch (Exception e)
{
i = j;
} catch (Exception e)
{
- throw new Error("Implementation bug in parseCigarString");
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_bug_parse_cigar_string"));
}
if (c >= 'a' && c <= 'z')
{
}
if (c >= 'a' && c <= 'z')
{
@@
-242,13
+250,13
@@
public abstract class CigarBase
}
else
{
}
else
{
- throw new Exception("Unexpected operation '" + c
- + "' in cigar string (position " + i + " in '"
- + cigarString + "'");
+ throw new Exception(MessageManager.formatMessage(
+ "exception.unexpected_operation_cigar_string_pos",
+ new String[] { new StringBuffer(c).toString(),
+ Integer.valueOf(i).toString(), cigarString }));
}
}
}
}
- return new Object[]
- { operation, range };
+ return new Object[] { operation, range };
}
/**
}
/**
@@
-267,7
+275,9
@@
public abstract class CigarBase
}
if (op != M && op != D && op != I)
{
}
if (op != M && op != D && op != I)
{
- throw new Error("Implementation error. Invalid operation string.");
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_invalid_operation_string"));
}
if (range == 0)
{
}
if (range == 0)
{
@@
-276,7
+286,7
@@
public abstract class CigarBase
if (range < 0)
{
throw new Error(
if (range < 0)
{
throw new Error(
- "Invalid range string (must be zero or positive number)");
+ MessageManager.getString("error.invalid_range_string"));
}
int lngth = 0;
if (operation == null)
}
int lngth = 0;
if (operation == null)
@@
-389,7
+399,8
@@
public abstract class CigarBase
if (start < 0 || start > end)
{
throw new Error(
if (start < 0 || start > end)
{
throw new Error(
- "Implementation Error: deleteRange out of bounds: start must be non-negative and less than end.");
+ MessageManager
+ .getString("error.implementation_error_delete_range_out_of_bounds"));
}
// find beginning
int cursor = 0; // mark the position for the current operation being edited.
}
// find beginning
int cursor = 0; // mark the position for the current operation being edited.
@@
-461,10
+472,13
@@
public abstract class CigarBase
}
break;
case D:
}
break;
case D:
- throw new Error("Implementation error."); // do nothing;
+ throw new Error(
+ MessageManager.getString("error.implementation_error")); // do
+ // nothing;
default:
default:
- throw new Error("Implementation Error! Unknown operation '"
- + oldops[o] + "'");
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_unknown_operation",
+ new String[] { new StringBuffer(oldops[o]).toString() }));
}
rlength -= remain;
remain = oldrange[++o]; // number of op characters left to edit
}
rlength -= remain;
remain = oldrange[++o]; // number of op characters left to edit
@@
-523,8
+537,7
@@
public abstract class CigarBase
vcursor += range[i];
break;
case D:
vcursor += range[i];
break;
case D:
- dr.addElement(new int[]
- { vcursor, cursor, range[i] });
+ dr.addElement(new int[] { vcursor, cursor, range[i] });
cursor += range[i];
}
}
cursor += range[i];
}
}