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Fix: refactor implementation and design smells #1088

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Fix: refactor implementation and design smells #1088

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62 changes: 27 additions & 35 deletions biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java
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Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,7 @@ public TranscriptSequence(GeneSequence parentDNASequence, AccessionID accessionI
setAccession(accessionID);
}

@Override
@Override
public int getLength() {
return Math.abs(this.getBioEnd() - this.getBioBegin()) + 1;
}
Expand Down Expand Up @@ -158,40 +158,7 @@ public ArrayList<ProteinSequence> getProteinCDSSequences() {
CDSSequence cdsSequence = cdsSequenceList.get(i);
String codingSequence = cdsSequence.getCodingSequence();
// logger.debug("CDS {} {} = {}", getStrand(), cdsSequence.getPhase(), codingSequence);
if (this.getStrand() == Strand.NEGATIVE) {
if (cdsSequence.phase == 1) {
codingSequence = codingSequence.substring(1, codingSequence.length());
} else if (cdsSequence.phase == 2) {
codingSequence = codingSequence.substring(2, codingSequence.length());
}
if (i < cdsSequenceList.size() - 1) {
CDSSequence nextCDSSequence = cdsSequenceList.get(i + 1);
if (nextCDSSequence.phase == 1) {
String nextCodingSequence = nextCDSSequence.getCodingSequence();
codingSequence = codingSequence + nextCodingSequence.substring(0, 1);
} else if (nextCDSSequence.phase == 2) {
String nextCodingSequence = nextCDSSequence.getCodingSequence();
codingSequence = codingSequence + nextCodingSequence.substring(0, 2);
}
}
} else {
if (cdsSequence.phase == 1) {
codingSequence = codingSequence.substring(1, codingSequence.length());
} else if (cdsSequence.phase == 2) {
codingSequence = codingSequence.substring(2, codingSequence.length());
}
if (i < cdsSequenceList.size() - 1) {
CDSSequence nextCDSSequence = cdsSequenceList.get(i + 1);
if (nextCDSSequence.phase == 1) {
String nextCodingSequence = nextCDSSequence.getCodingSequence();
codingSequence = codingSequence + nextCodingSequence.substring(0, 1);
} else if (nextCDSSequence.phase == 2) {
String nextCodingSequence = nextCDSSequence.getCodingSequence();
codingSequence = codingSequence + nextCodingSequence.substring(0, 2);
}
}
}

codingSequence = getCodingSequence(proteinSequenceList, codingSequence, i);

// logger.debug("Coding Sequence: {}", codingSequence);

Expand All @@ -211,6 +178,31 @@ public ArrayList<ProteinSequence> getProteinCDSSequences() {
return proteinSequenceList;
}

/**
* Helper method to reduce duplication and complexity in the getProteinCDSSequences method
*
* @return string
*/
private String getCodingSequence(ArrayList<ProteinSequence> proteinSequenceList, String codingSequence, int index) {
CDSSequence cdsSequence = cdsSequenceList.get(index);
if (cdsSequence.phase == 1) {
codingSequence = codingSequence.substring(1, codingSequence.length());
} else if (cdsSequence.phase == 2) {
codingSequence = codingSequence.substring(2, codingSequence.length());
}
if (index < cdsSequenceList.size() - 1) {
CDSSequence nextCDSSequence = cdsSequenceList.get(index + 1);
if (nextCDSSequence.phase == 1) {
String nextCodingSequence = nextCDSSequence.getCodingSequence();
codingSequence = codingSequence + nextCodingSequence.substring(0, 1);
} else if (nextCDSSequence.phase == 2) {
String nextCodingSequence = nextCDSSequence.getCodingSequence();
codingSequence = codingSequence + nextCodingSequence.substring(0, 2);
}
}
return codingSequence;
}

/**
* Get the stitched together CDS sequences then maps to the cDNA
* @return
Expand Down
26 changes: 22 additions & 4 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/AtomPositionMap.java
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Expand Up @@ -198,16 +198,34 @@ public int getLength(int positionA, int positionB, String startingChain) {
int count = 0;
// Inefficient search
for (Map.Entry<ResidueNumber, Integer> entry : treeMap.entrySet()) {
if (entry.getKey().getChainName().equals(startingChain)
&& positionStart <= entry.getValue()
&& entry.getValue() <= positionEnd)
{
if (equalToStartingChain(entry,startingChain) && inRange(entry,positionStart,positionEnd)){
count++;
}
}
return count;
}

/**
* Checks if the entry is equal to the starting chain
* @param entry Map of residue number
* @param startingChain Case-sensitive chain
* @return True if the entry is equal to the starting chain
*/
private boolean equalToStartingChain(Map.Entry<ResidueNumber, Integer> entry, String startingChain){
return entry.getKey().getChainName().equals(startingChain);
}

/**
* Checks if the entry is in a specific range
* @param entry Map of residue number
* @param positionStart index of the start position
* @param positionEnd index of the end position
* @return True if the entry is in the range
*/
private boolean inRange(Map.Entry<ResidueNumber, Integer> entry, int positionStart, int positionEnd){
return positionStart <= entry.getValue() && entry.getValue() <= positionEnd;
}


/**
* Calculates the number of residues of the specified chain in a given range.
Expand Down
9 changes: 3 additions & 6 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java
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Original file line number Diff line number Diff line change
Expand Up @@ -43,11 +43,7 @@
import org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl;
import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer;
import org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer;
import org.biojava.nbio.structure.cluster.Subunit;
import org.biojava.nbio.structure.cluster.SubunitCluster;
import org.biojava.nbio.structure.cluster.SubunitClusterer;
import org.biojava.nbio.structure.cluster.SubunitClustererParameters;
import org.biojava.nbio.structure.cluster.SubunitExtractor;
import org.biojava.nbio.structure.cluster.*;
import org.biojava.nbio.structure.contact.Pair;
import org.biojava.nbio.structure.geometry.SuperPositions;
import org.biojava.nbio.structure.geometry.UnitQuaternions;
Expand Down Expand Up @@ -104,7 +100,8 @@ public static QsAlignResult align(List<Subunit> s1, List<Subunit> s2,
continue;

// Use structural alignment to match the subunit clusters
if (c1.get(i).mergeStructure(c2.get(j),cParams)) {
SubunitClusterMerge subunitClusterMerge = new SubunitClusterMerge(c1.get(i));
if (subunitClusterMerge.mergeStructure(c2.get(j),cParams)) {
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@josemduarte josemduarte Apr 8, 2024

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In my opinion it was more readable before, as you could see the i/j merging in a single line. Would you have a strong reason for this change?

clusterMap.put(i, j);
}
}
Expand Down
3 changes: 2 additions & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PdbPairsMessage.java
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Expand Up @@ -25,6 +25,7 @@
package org.biojava.nbio.structure.align.xml;

import org.biojava.nbio.structure.align.client.PdbPair;
import org.biojava.nbio.structure.align.fatcat.FatCatRigid;

import java.io.StringWriter;
import java.util.SortedSet;
Expand All @@ -38,7 +39,7 @@ public class PdbPairsMessage {

public PdbPairsMessage(){

method = PdbPairXMLConverter.DEFAULT_METHOD_NAME;
method = FatCatRigid.algorithmName;
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@josemduarte josemduarte Apr 8, 2024

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I think it was intended to point to DEFAULT_METHOD_NAME. Then there's a constant that's specific for the default.


pairs = new TreeSet<PdbPair>();

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