Skip to content

Added Indexes on FeatureList #2

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
CarmeloFoti wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Added Indexes on FeatureList #2

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
282c5ee
Added indexes on FeatureList
CarmeloFoti Jun 6, 2012
d8b3394
Bug fixed
CarmeloFoti Jul 13, 2012
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
19 changes: 13 additions & 6 deletions biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/Feature.java
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
package org.biojava3.genome.parsers.gff;

import java.util.HashMap;
import java.util.List;
import java.util.Map;


/**
Expand All @@ -17,7 +19,7 @@ public class Feature implements FeatureI {
private double mScore; //or . if none
private int mFrame; //0,1,2
private String mAttributes; //any trailing stuff
private HashMap<String, Object> mUserMap;
private HashMap<String, String> mUserMap;

/**
* Get the sequence name. (GFF field 1). Note that feature objects have
Expand Down Expand Up @@ -129,7 +131,7 @@ public Feature(Feature feature) {
mFrame = feature.mFrame;
mAttributes = feature.mAttributes;
initAttributeHashMap();
mUserMap = new HashMap<String, Object>(feature.mUserMap);
mUserMap = new HashMap<String, String>(feature.mUserMap);
}

/**
Expand All @@ -153,7 +155,7 @@ public Feature(String seqname, String source, String type, Location location, Do
mFrame = frame;
mAttributes = attributes;
initAttributeHashMap();
mUserMap = new HashMap<String, Object>();
mUserMap = new HashMap<String, String>();

}

Expand All @@ -170,11 +172,11 @@ public Feature(String seqname, String source, String type, Location location, Do
*
* @return The user HashMap.
*/
public HashMap<String, Object> userData() {
public HashMap<String, String> userData() {
return mUserMap;
}

HashMap<String,String> attributeHashMap = new HashMap<String,String>();
HashMap<String,String> attributeHashMap = new HashMap<String,String>();

private void initAttributeHashMap(){
String[] values = mAttributes.split(";");
Expand All @@ -193,7 +195,6 @@ private void initAttributeHashMap(){
}
attributeHashMap.put(data[0].trim(), value);
}

}

/**
Expand Down Expand Up @@ -304,4 +305,10 @@ public static void main(String args[])
// assert f.getAttribute( "transcript").equals( "gene_id fantom2" );
//Log.log( "passed test." );
}

@Override
public HashMap<String, String> getAttributes() {

return attributeHashMap;
}
}
4 changes: 3 additions & 1 deletion biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/FeatureI.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,8 @@ public interface FeatureI
*
* @return The user HashMap.
*/
public HashMap<String, Object> userData();
public HashMap<String, String> userData();

public HashMap<String, String> getAttributes();

}
Loading