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JAL-1807 explicit imports (jalview.io.*)
[jalview.git]
/
src
/
jalview
/
io
/
ModellerDescription.java
diff --git
a/src/jalview/io/ModellerDescription.java
b/src/jalview/io/ModellerDescription.java
index
30f46bf
..
9a3453f
100755
(executable)
--- a/
src/jalview/io/ModellerDescription.java
+++ b/
src/jalview/io/ModellerDescription.java
@@
-20,7
+20,11
@@
*/
package jalview.io;
*/
package jalview.io;
-import jalview.datamodel.*;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+
+import com.stevesoft.pat.Regex;
public class ModellerDescription
{
public class ModellerDescription
{
@@
-95,8
+99,7
@@
public class ModellerDescription
private resCode validResidueCode(String field)
{
Integer val = null;
private resCode validResidueCode(String field)
{
Integer val = null;
- com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex(
- "\\s*((([-0-9]+).?)|FIRST|LAST|@)");
+ Regex r = new Regex("\\s*((([-0-9]+).?)|FIRST|LAST|@)");
if (!r.search(field))
{
if (!r.search(field))
{
@@
-107,7
+110,7
@@
public class ModellerDescription
{
value = r.stringMatched(1);
}
{
value = r.stringMatched(1);
}
- // jalview.bin.Cache.log.debug("from '" + field + "' matched '" + value +
+ // Cache.log.debug("from '" + field + "' matched '" + value +
// "'");
try
{
// "'");
try
{
@@
-162,7
+165,7
@@
public class ModellerDescription
}
else
{
}
else
{
- // jalview.bin.Cache.log.debug(
+ // Cache.log.debug(
// "Ignoring non-Modeller description: invalid integer-like
// field '" + field + "'");
type = -1; /* invalid field! - throw the FieldSet away */
// "Ignoring non-Modeller description: invalid integer-like
// field '" + field + "'");
type = -1; /* invalid field! - throw the FieldSet away */
@@
-273,8
+276,7
@@
public class ModellerDescription
if (seq.getDatasetSequence() != null
&& seq.getDatasetSequence().getDBRef() != null)
{
if (seq.getDatasetSequence() != null
&& seq.getDatasetSequence().getDBRef() != null)
{
- jalview.datamodel.DBRefEntry[] dbr = seq.getDatasetSequence()
- .getDBRef();
+ DBRefEntry[] dbr = seq.getDatasetSequence().getDBRef();
int i, j;
for (i = 0, j = dbr.length; i < j; i++)
{
int i, j;
for (i = 0, j = dbr.length; i < j; i++)
{
@@
-284,8
+286,7
@@
public class ModellerDescription
// ModellerField
// JBPNote Need to get info from the user about whether the sequence
// is the one being modelled, or if it is a template.
// ModellerField
// JBPNote Need to get info from the user about whether the sequence
// is the one being modelled, or if it is a template.
- if (dbr[i].getSource()
- .equals(jalview.datamodel.DBRefSource.PDB))
+ if (dbr[i].getSource().equals(DBRefSource.PDB))
{
fields.put(Fields[LOCALID], dbr[i].getAccessionId());
t = 2;
{
fields.put(Fields[LOCALID], dbr[i].getAccessionId());
t = 2;