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JAL-1563 Modified Uniprot data column configurations and improved implementation...
author
tcofoegbu
<tcnofoegbu@dundee.ac.uk>
Wed, 27 Apr 2016 12:57:28 +0000
(13:57 +0100)
committer
tcofoegbu
<tcnofoegbu@dundee.ac.uk>
Wed, 27 Apr 2016 12:57:28 +0000
(13:57 +0100)
resources/fts/uniprot_data_columns.txt
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src/jalview/fts/api/FTSDataColumnI.java
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src/jalview/fts/core/FTSRestClient.java
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src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
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src/jalview/fts/service/uniprot/UniprotFTSPanel.java
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diff --git
a/resources/fts/uniprot_data_columns.txt
b/resources/fts/uniprot_data_columns.txt
index
40e28e4
..
a7365c5
100644
(file)
--- a/
resources/fts/uniprot_data_columns.txt
+++ b/
resources/fts/uniprot_data_columns.txt
@@
-23,10
+23,10
@@
g17;Date of;17
g18;Family & Domain;18
#
_data_column.primary_key;entry name
g18;Family & Domain;18
#
_data_column.primary_key;entry name
-_data_column.default_response_page_size;100
+_data_column.default_response_page_size;150
#
_data_column.name
#
_data_column.name
-_data_column.code
+_data_column.code|_data_column.alt_code (optional: used for specifying search code when different from original code)
_data_column.group_id
_data_column.data_type
_data_column.min_col_width
_data_column.group_id
_data_column.data_type
_data_column.min_col_width
@@
-35,7
+35,7
@@
_data_column.preferred_col_width
_data_column.is_shown_by_default
_data_column.is_searchable
Entry Name;entry name;String;g3;90;150;95;true;true
_data_column.is_shown_by_default
_data_column.is_searchable
Entry Name;entry name;String;g3;90;150;95;true;true
-Protein names;protein names;String;g3;300;1500;500;true;true
+Protein names;protein names|protein name;String;g3;300;1500;500;true;true
Gene Names;genes;String;g3;50;1000;95;true;true
Organism;organism;String;g3;50;1000;95;true;true
Organism ID;organism-id;int;g3;60;100;80;false;true
Gene Names;genes;String;g3;50;1000;95;true;true
Organism;organism;String;g3;50;1000;95;true;true
Organism ID;organism-id;int;g3;60;100;80;false;true
@@
-53,7
+53,7
@@
Mass spectrometry;comment(MASS SPECTROMETRY);String;g7;50;1000;95;false;false
Polymorphism;comment(POLYMORPHISM);String;g7;50;1000;95;false;false
RNA editing;comment(RNA EDITING);String;g7;50;1000;95;false;false
Sequence caution;comment(SEQUENCE CAUTION);String;g7;50;1000;95;false;false
Polymorphism;comment(POLYMORPHISM);String;g7;50;1000;95;false;false
RNA editing;comment(RNA EDITING);String;g7;50;1000;95;false;false
Sequence caution;comment(SEQUENCE CAUTION);String;g7;50;1000;95;false;false
-Length;length;int;g7;50;100;95;false;true
+Length;length;int;g7;50;100;65;true;true
Mass;mass;String;g7;50;100;80;false;true
Sequence;sequence;String;g7;50;1000;95;false;true
Alternative sequence;feature(ALTERNATIVE SEQUENCE);String;g7;50;1000;95;false;false
Mass;mass;String;g7;50;100;80;false;true
Sequence;sequence;String;g7;50;1000;95;false;true
Alternative sequence;feature(ALTERNATIVE SEQUENCE);String;g7;50;1000;95;false;false
@@
-87,8
+87,8
@@
Caution;comment(CAUTION);String;g6;50;1000;95;false;false
Miscellaneous [CC];comment(GENERAL);String;g6;50;1000;95;false;false
Keywords;keywords;String;g6;50;1000;95;false;true
Protein existence;existence;String;g6;50;1000;95;false;true
Miscellaneous [CC];comment(GENERAL);String;g6;50;1000;95;false;false
Keywords;keywords;String;g6;50;1000;95;false;true
Protein existence;existence;String;g6;50;1000;95;false;true
-Status;reviewed;String;g6;50;1000;95;false;true
-ALL;name;String;g7;50;1000;95;false;true;
+Status;reviewed;String;g6;50;100;95;true;true
+ALL;Search All;String;g7;50;1000;95;false;true;
Subunit structure [CC];comment(SUBUNIT);String;g9;50;1000;95;false;false
Interacts with;interactor;String;g9;50;1000;95;false;true
Developmental stage;comment(DEVELOPMENTAL STAGE);String;g10;50;1000;95;false;false
Subunit structure [CC];comment(SUBUNIT);String;g9;50;1000;95;false;false
Interacts with;interactor;String;g9;50;1000;95;false;true
Developmental stage;comment(DEVELOPMENTAL STAGE);String;g10;50;1000;95;false;false
@@
-126,8
+126,8
@@
Beta strand;feature(BETA STRAND);String;g15;50;1000;95;false;false
Helix;feature(HELIX);String;g15;50;1000;95;false;false
Turn;feature(TURN);String;g15;50;1000;95;false;false
PubMed ID;citation;String;g16;50;1000;95;false;true
Helix;feature(HELIX);String;g15;50;1000;95;false;false
Turn;feature(TURN);String;g15;50;1000;95;false;false
PubMed ID;citation;String;g16;50;1000;95;false;true
-Date of creation;created;String;g17;80;150;100;true;true
-Date of last modification;last-modified;String;g17;80;150;100;true;true
+Date of creation;created;String;g17;80;150;100;false;true
+Date of last modification;last-modified;String;g17;80;150;100;false;true
Date of last sequence modification;sequence-modified;String;g17;80;150;100;false;true
Version (entry);version(entry);int;g17;80;100;80;false;false
Domain [CC];comment(DOMAIN);String;g18;80;1000;95;false;false
Date of last sequence modification;sequence-modified;String;g17;80;150;100;false;true
Version (entry);version(entry);int;g17;80;100;80;false;false
Domain [CC];comment(DOMAIN);String;g18;80;1000;95;false;false
diff --git
a/src/jalview/fts/api/FTSDataColumnI.java
b/src/jalview/fts/api/FTSDataColumnI.java
index
ea30d01
..
7741d73
100644
(file)
--- a/
src/jalview/fts/api/FTSDataColumnI.java
+++ b/
src/jalview/fts/api/FTSDataColumnI.java
@@
-44,6
+44,13
@@
public interface FTSDataColumnI
public String getCode();
/**
public String getCode();
/**
+ * Returns the alternative code value for the data column
+ *
+ * @return the data column's code
+ */
+ public String getAltCode();
+
+ /**
* Returns the minimum width of the data column
*
* @return the data column's minimum width
* Returns the minimum width of the data column
*
* @return the data column's minimum width
diff --git
a/src/jalview/fts/core/FTSRestClient.java
b/src/jalview/fts/core/FTSRestClient.java
index
0605fef
..
e3e2354
100644
(file)
--- a/
src/jalview/fts/core/FTSRestClient.java
+++ b/
src/jalview/fts/core/FTSRestClient.java
@@
-131,7
+131,14
@@
public abstract class FTSRestClient implements FTSRestClientI
@Override
public String getCode()
{
@Override
public String getCode()
{
- return lineData[1];
+ return lineData[1].split("\\|")[0];
+ }
+
+ @Override
+ public String getAltCode()
+ {
+ return lineData[1].split("\\|").length > 1 ? lineData[1]
+ .split("\\|")[1] : getCode();
}
@Override
}
@Override
diff --git
a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
index
c8e21e0
..
7eda9f8
100644
(file)
--- a/
src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
+++ b/
src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
@@
-58,8
+58,12
@@
public class UniProtFTSRestClient extends FTSRestClient
int responseSize = (uniportRestRequest.getResponseSize() == 0) ? getDefaultResponsePageSize()
: uniportRestRequest.getResponseSize();
int responseSize = (uniportRestRequest.getResponseSize() == 0) ? getDefaultResponsePageSize()
: uniportRestRequest.getResponseSize();
- String query = uniportRestRequest.getFieldToSearchBy() + ":"
- + uniportRestRequest.getSearchTerm();
+ String query = uniportRestRequest.getFieldToSearchBy()
+ .equalsIgnoreCase("Search All") ? uniportRestRequest
+ .getSearchTerm()
+ : uniportRestRequest.getFieldToSearchBy() + ":"
+ + uniportRestRequest.getSearchTerm();
+
// + (uniportRestRequest.isAllowUnpublishedEntries() ? ""
// : " AND status:REL");
// System.out.println(">>>>> Query : " + query);
// + (uniportRestRequest.isAllowUnpublishedEntries() ? ""
// : " AND status:REL");
// System.out.println(">>>>> Query : " + query);
diff --git
a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
index
dcef358
..
21343d3
100644
(file)
--- a/
src/jalview/fts/service/uniprot/UniprotFTSPanel.java
+++ b/
src/jalview/fts/service/uniprot/UniprotFTSPanel.java
@@
-63,7
+63,7
@@
public class UniprotFTSPanel extends GFTSPanel
long startTime = System.currentTimeMillis();
String searchTarget = ((FTSDataColumnI) cmb_searchTarget
long startTime = System.currentTimeMillis();
String searchTarget = ((FTSDataColumnI) cmb_searchTarget
- .getSelectedItem()).getCode();
+ .getSelectedItem()).getAltCode();
wantedFields = UniProtFTSRestClient.getInstance()
.getAllDefaulDisplayedDataColumns();
wantedFields = UniProtFTSRestClient.getInstance()
.getAllDefaulDisplayedDataColumns();