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'STRAP:multiple sequence alignments ' | ||||||||
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java.lang.Object charite.christo.metannogen.MObject charite.christo.metannogen.MReaction
public class MReaction
First invokation of a getter my take several Mikroseconds. Then all outputs are cached and take Nanos. All metabolite and compartment Strings are finalized and can be compared by identity instead of equals which is faster.
Field Summary | |
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static MReaction[] |
NONE
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Fields inherited from interface charite.christo.metannogen.Reaction |
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DIRECTION_BACKWARD, DIRECTION_FORWARD, DIRECTION_REVERSIBLE, EQUALS_IGNORE_COMPARTMENT, EQUALS_IGNORE_ORIENTATION, EQUALS_IGNORE_PROTON, EQUALS_IGNORE_STOICHIOMETRY, EQUALS_RECORD_DIFFERENCES, FILTER_NOT_EXCLUDED, FILTER_REJECTED_DATASETS, TEXT_HUMAN_READABLE, TEXT_NO_COMPARTMENT, TEXT_SORT_METABOLITES, UNIQUE |
Fields inherited from interface charite.christo.interfaces.HasRendererText |
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JLIST |
Constructor Summary | |
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MReaction()
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MReaction(byte[] text)
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MReaction(byte[] txt,
int begin,
int end)
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MReaction(CharSequence text)
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MReaction(String[] mmS,
int[] stoichS,
String[] ccS,
String[] mmP,
int[] stoichP,
String[] ccP)
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Method Summary | |
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boolean |
areAllCompartmentsTranslated()
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boolean |
areAllSpeciesTranslated()
Short for Integer.parsInt(getAttribute(key)). |
boolean |
assertIntern()
Checks whether the arrays have the same length and whether for all Strings s=s.intern(); |
boolean |
equals(Reaction r,
long options)
Comparison |
static String |
equationHumanReadable(ByteArray ba,
boolean sumFormula)
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float[] |
floatValues()
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String[] |
getAllNames()
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String[] |
getBraceExpansionID()
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Object[] |
getChildren()
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Color |
getColor()
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CharSequence |
getComment()
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String |
getCompartmentOfSpecies(String m)
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String |
getCompartmentOfSpeciesP(String m)
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String |
getCompartmentOfSpeciesS(String m)
Returns null if the given metabolite is not part of the reaction. |
String[] |
getCompartmentsP()
List of Compartments for products. |
String[] |
getCompartmentsS()
List of reactants |
String[] |
getCompartmentsWithEnzyme()
Alle compartments fur diese Reaktionsgleichung, sorted alphabetically In der Implementierung wird getReactionsWithThisStoichiometry() iteriert und eine Liste aller compartments erstellt. |
int |
getConfidence()
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String[] |
getDatasetFields()
If the reaction is created from a Dataset then return the dataset fields. |
float |
getDeltaG()
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int |
getDirection()
See DIRECTION_FORWARD, DIRECTION_BACKWARD, DIRECTION_REVERSIBLE |
EC_Class[] |
getEC_classes()
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String[] |
getEC()
Array of EC-numbers or an array of length 0. |
MReaction[] |
getIdenticalReactionsNC()
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static String[] |
getIDsForProton()
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String |
getInfoText()
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static String[] |
getLastEqualsDifferingMetabolite()
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String |
getName()
The human readable name of the reaction. |
String[] |
getOrthologies()
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Pathway[] |
getPathways()
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String[] |
getProducts()
List of products The following Arrays have exactly the same size: getCompartmentsP() getProducts() getSpeciesP() getStoichiometriesP() |
MReaction |
getReactionMetabolitesMappedNC(Map<String,String> mapMetabolites)
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MReaction[] |
getReactionsWithThisStoichiometry()
Die Grundidee ist, dass initial ein Array von Reaktionen generiert wird, bei der jede Stoichiometrie nur einmal auftaucht. |
String |
getRendererText(int options)
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MSpecies[] |
getSpecies()
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MSpecies[] |
getSpeciesP()
List of products |
MSpecies[] |
getSpeciesS()
List of reactants |
int[] |
getStoichiometriesP()
Stoichiometries of products. |
int[] |
getStoichiometriesS()
Stoichiometries of reactants. |
int |
getStoichiometryP(String metabolite,
String compartment)
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int |
getStoichiometryS(String metabolite,
String compartment)
Compartment may be null. |
String[] |
getSubstrates()
List of reactants The following Arrays have exactly the same size: getCompartmentsS() getSubstrates() getSpeciesS() getStoichiometriesS() |
String[] |
getSubstratesAndProducts()
All metabolites as a unique sorted list |
String[] |
getSubstratesAndProductsWithoutProton()
Metabolite IDs, skip hydrogen |
int |
getSubstratesAndProductsWithoutProtonHashCode()
Dadurch wird die equals Methode extrem schnell |
String[] |
getSubstratesAndProductsWithoutProtonMapped()
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TabItemTipIcon |
getTabItemTipIcon(MouseEvent ev)
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boolean |
hasChildren()
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int |
hashCode(Object o)
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boolean |
isAlreadyInOtherNetwork()
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boolean |
isBiomass()
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boolean |
isExcluded()
Exists but should not be used in file export. |
boolean |
isGeneral()
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boolean |
isReversible()
Identical to getDirection()==DIRECTION_REVERSIBLE |
boolean |
isTransport()
True if reactants and products have different compartments. |
static void |
main(String[] argv)
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void |
setAlreadyInOtherNetwork(boolean b)
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void |
setBraceExpansionID(String[] braceID)
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void |
setColor(Color color)
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void |
setComment(CharSequence s)
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MReaction |
setCompartmentDictionary(Map<String,String> map)
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void |
setConfidence(int c)
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void |
setDatasetFields(String[] fields)
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MReaction |
setDefaultCompartment(String compartment)
When parsing from text, metabolites without underscor_compartment are assigned the default compartment. |
void |
setDefinition(CharSequence s)
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void |
setDeltaG(float dg)
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void |
setDirection(int dir)
See DIRECTION_FORWARD, DIRECTION_BACKWARD, DIRECTION_REVERSIBLE |
void |
setEC(CharSequence s)
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void |
setEC(String[] ec)
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void |
setEquation(CharSequence text)
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void |
setExcluded(boolean yesNo)
Exists but should not be used in file export |
static void |
setIDsForProton(String[] idsOfProton)
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MReaction |
setMetaboliteDictionary(Map<String,String> map)
Used to convert metabolite ID's when parsing from String |
void |
setOrthologies(CharSequence s)
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void |
setPathways(Pathway[] ss)
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void |
setReactionsWithThisStoichiometry(Reaction[] rr)
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void |
setSubstratesOrProducts(String[] metabolite,
int[] stoich,
String[] compart,
boolean isProduct)
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MSpecies |
speciesForID(CharSequence id)
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MSpecies[] |
speciesFromIDs(CharSequence[] ss)
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String |
toText(int options)
Options may be 0 or TEXT_HUMAN_READABLE |
String |
toTextSorted(long options)
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MReaction |
translateMetabolitesAndCompartments(Map<String,String> mapM,
Map<String,String> mapC)
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Methods inherited from class charite.christo.metannogen.MObject |
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clone, getAttribute, getAttributeF, getAttributeI, getAttributes, getClientProperty, getClientPropertyMapAsString, getCollection, getEntireText, getHaystacksForStringSearch, getID, getIDMapped, getIDMappedSimilar, getParent, getTopAncestor, getTopAncestorID, putClientProperty, setAttributes, setCollection, setID, setName, setParent, setTextBlock, toString |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface charite.christo.metannogen.Reaction |
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getAttribute, getAttributeF, getAttributeI, getAttributes, getClientProperty, getCollection, getID, putClientProperty |
Methods inherited from interface charite.christo.interfaces.HasID |
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getID |
Methods inherited from interface charite.christo.DialogStringMatch.Interface |
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getHaystacksForStringSearch |
Field Detail |
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public static final MReaction[] NONE
Constructor Detail |
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public MReaction()
public MReaction(CharSequence text)
public MReaction(byte[] text)
public MReaction(byte[] txt, int begin, int end)
public MReaction(String[] mmS, int[] stoichS, String[] ccS, String[] mmP, int[] stoichP, String[] ccP)
Method Detail |
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public void setOrthologies(CharSequence s)
public void setDefinition(CharSequence s)
public void setComment(CharSequence s)
public final CharSequence getComment()
public MReaction[] getReactionsWithThisStoichiometry()
Reaction
getReactionsWithThisStoichiometry
in interface Reaction
public void setReactionsWithThisStoichiometry(Reaction[] rr)
setReactionsWithThisStoichiometry
in interface Reaction
public String[] getCompartmentsWithEnzyme()
Reaction
getCompartmentsWithEnzyme
in interface Reaction
public boolean isTransport()
Reaction
isTransport
in interface Reaction
public boolean isBiomass()
isBiomass
in interface Reaction
public float getDeltaG()
getDeltaG
in interface Reaction
public void setDeltaG(float dg)
setDeltaG
in interface Reaction
public MSpecies speciesForID(CharSequence id)
public MSpecies[] speciesFromIDs(CharSequence[] ss)
public MSpecies[] getSpeciesS()
Reaction
getSpeciesS
in interface Reaction
public MSpecies[] getSpeciesP()
Reaction
getSpeciesP
in interface Reaction
public MSpecies[] getSpecies()
public String[] getSubstratesAndProductsWithoutProtonMapped()
public String[] getSubstratesAndProductsWithoutProton()
getSubstratesAndProductsWithoutProton
in interface Reaction
public int getConfidence()
getConfidence
in interface Reaction
public void setConfidence(int c)
public MReaction setDefaultCompartment(String compartment)
public void setEquation(CharSequence text)
public static void setIDsForProton(String[] idsOfProton)
public static String[] getIDsForProton()
public MReaction setMetaboliteDictionary(Map<String,String> map)
public MReaction setCompartmentDictionary(Map<String,String> map)
public String[] getSubstratesAndProducts()
getSubstratesAndProducts
in interface Reaction
public String[] getProducts()
Reaction
getProducts
in interface Reaction
public String[] getSubstrates()
Reaction
getSubstrates
in interface Reaction
public String[] getCompartmentsP()
Reaction
getCompartmentsP
in interface Reaction
public String[] getCompartmentsS()
Reaction
getCompartmentsS
in interface Reaction
public String getCompartmentOfSpeciesS(String m)
Reaction
getCompartmentOfSpeciesS
in interface Reaction
public String getCompartmentOfSpeciesP(String m)
getCompartmentOfSpeciesP
in interface Reaction
public String getCompartmentOfSpecies(String m)
public int[] getStoichiometriesS()
Reaction
getStoichiometriesS
in interface Reaction
public int[] getStoichiometriesP()
Reaction
getStoichiometriesP
in interface Reaction
public int getStoichiometryS(String metabolite, String compartment)
Reaction
getStoichiometryS
in interface Reaction
public int getStoichiometryP(String metabolite, String compartment)
getStoichiometryP
in interface Reaction
public void setSubstratesOrProducts(String[] metabolite, int[] stoich, String[] compart, boolean isProduct)
public String toText(int options)
Reaction
toText
in interface Reaction
public int getSubstratesAndProductsWithoutProtonHashCode()
Reaction
getSubstratesAndProductsWithoutProtonHashCode
in interface Reaction
public boolean equals(Reaction r, long options)
Reaction
equals
in interface Reaction
public static final String[] getLastEqualsDifferingMetabolite()
public boolean areAllSpeciesTranslated()
Reaction
areAllSpeciesTranslated
in interface Reaction
public boolean areAllCompartmentsTranslated()
public MReaction translateMetabolitesAndCompartments(Map<String,String> mapM, Map<String,String> mapC)
public static void main(String[] argv)
public final String getName()
Reaction
getName
in interface HasName
getName
in interface Reaction
getName
in class MObject
public final int hashCode(Object o)
public String toTextSorted(long options)
public final float[] floatValues()
public boolean isGeneral()
public void setDirection(int dir)
Reaction
setDirection
in interface Reaction
public int getDirection()
Reaction
getDirection
in interface Reaction
public boolean isReversible()
Reaction
isReversible
in interface Reaction
public String[] getEC()
Reaction
getEC
in interface Reaction
public void setEC(CharSequence s)
public void setEC(String[] ec)
public EC_Class[] getEC_classes()
public String[] getOrthologies()
public void setPathways(Pathway[] ss)
public Pathway[] getPathways()
public boolean hasChildren()
hasChildren
in interface HasChildren
public Object[] getChildren()
getChildren
in interface HasChildren
public MReaction[] getIdenticalReactionsNC()
public final String getInfoText()
getInfoText
in interface HasInfoText
public final Color getColor()
getColor
in interface Colored
public final void setColor(Color color)
setColor
in interface Colored
public String getRendererText(int options)
getRendererText
in interface HasRendererText
public TabItemTipIcon getTabItemTipIcon(MouseEvent ev)
getTabItemTipIcon
in interface TabItemTipIcon.Interface
public MReaction getReactionMetabolitesMappedNC(Map<String,String> mapMetabolites)
public void setAlreadyInOtherNetwork(boolean b)
public boolean isAlreadyInOtherNetwork()
public void setExcluded(boolean yesNo)
Reaction
setExcluded
in interface Reaction
public boolean isExcluded()
Reaction
isExcluded
in interface Reaction
public String[] getDatasetFields()
Reaction
getDatasetFields
in interface Reaction
public void setDatasetFields(String[] fields)
public boolean assertIntern()
public static String equationHumanReadable(ByteArray ba, boolean sumFormula)
public String[] getAllNames()
public void setBraceExpansionID(String[] braceID)
public String[] getBraceExpansionID()
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'STRAP:multiple sequence alignments ' | ||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |