#314 Missing enumeration values in case

[William S Noble]

/Users/nobleadmin/proj/crux/trunk/src/model/Match.cpp:237:11: warning: 12 enumeration values not handled in switch: 'FILE_IDX_COL', 'DELTA_LCN_COL', 'ELUTION_WINDOW_COL'... [-Wswitch]
switch ((MATCH_COLUMNS_T)column_idx) {
^
1 warning generated.

/Users/nobleadmin/proj/crux/trunk/src/io/MatchFileWriter.cpp:181:11: warning: 10 enumeration values not handled in switch: 'BULLSEYE_COMMAND', 'MIXMAX_COMMAND', 'TDC_COMMAND'... [-Wswitch]
switch (command){
^
/Users/nobleadmin/proj/crux/trunk/src/io/MatchFileWriter.cpp:307:11: warning: 11 enumeration values not handled in switch: 'BULLSEYE_COMMAND', 'MIXMAX_COMMAND', 'TDC_COMMAND'... [-Wswitch]
switch (command){
^
2 warnings generated.

/Users/nobleadmin/proj/crux/trunk/src/model/MatchCollection.cpp:185:11: warning: 21 enumeration values not handled in switch: 'SP', 'XCORR', 'XCORR_FIRST'... [-Wswitch]
switch (score_type) {
^
/Users/nobleadmin/proj/crux/trunk/src/model/MatchCollection.cpp:1646:13: warning: 13 enumeration values not handled in switch: 'XCORR_FIRST', 'XCORR_SECOND', 'DECOY_EVALUE_PEPTIDE_QVALUE'... [-Wswitch]
switch (score_type) {
^
/Users/nobleadmin/proj/crux/trunk/src/model/MatchCollection.cpp:1771:13: warning: 15 enumeration values not handled in switch: 'XCORR_FIRST', 'XCORR_SECOND', 'DECOY_EVALUE_QVALUE'... [-Wswitch]
switch (score_type) {
^
3 warnings generated.

/Users/nobleadmin/proj/crux/trunk/src/model/Protein.cpp:598:10: warning: enumeration value 'PEPTIDE_REVERSE_DECOYS' not handled in switch [-Wswitch]
switch(decoy_type){
^
1 warning generated.

[William S Noble]

Here is a full listing from the Clang compiler with revision 16852:

/Users/nobleadmin/proj/crux/trunk/src/app/AssignConfidenceApplication.cpp:426:13: warning: 23 enumeration values not handled in switch: 'INVALID_COMMAND', 'BULLSEYE_COMMAND', 'QVALUE_COMMAND'... [-Wswitch]
switch (command){
^
/Users/nobleadmin/proj/crux/trunk/src/app/AssignConfidenceApplication.cpp:444:11: warning: 23 enumeration values not handled in switch: 'INVALID_COMMAND', 'BULLSEYE_COMMAND', 'QVALUE_COMMAND'... [-Wswitch]
switch (command){
^
/Users/nobleadmin/proj/crux/trunk/src/app/AssignConfidenceApplication.cpp:468:11: warning: 23 enumeration values not handled in switch: 'INVALID_COMMAND', 'BULLSEYE_COMMAND', 'QVALUE_COMMAND'... [-Wswitch]
switch (command){
^
/Users/nobleadmin/proj/crux/trunk/src/model/Match.cpp:240:11: warning: 33 enumeration values not handled in switch: 'FILE_IDX_COL', 'DELTA_LCN_COL', 'ELUTION_WINDOW_COL'... [-Wswitch]
switch ((MATCH_COLUMNS_T)column_idx) {
^
/Users/nobleadmin/proj/crux/trunk/src/io/MatchFileWriter.cpp:191:11: warning: 10 enumeration values not handled in switch: 'BULLSEYE_COMMAND', 'MIXMAX_COMMAND', 'TDC_COMMAND'... [-Wswitch]
switch (command){
^
/Users/nobleadmin/proj/crux/trunk/src/io/MatchFileWriter.cpp:317:11: warning: 11 enumeration values not handled in switch: 'BULLSEYE_COMMAND', 'MIXMAX_COMMAND', 'TDC_COMMAND'... [-Wswitch]
switch (command){
^
/Users/nobleadmin/proj/crux/trunk/src/model/MatchCollection.cpp:185:11: warning: 21 enumeration values not handled in switch: 'SP', 'XCORR', 'XCORR_FIRST'... [-Wswitch]
switch (score_type) {
^
/Users/nobleadmin/proj/crux/trunk/src/model/MatchCollection.cpp:1655:13: warning: 13 enumeration values not handled in switch: 'XCORR_FIRST', 'XCORR_SECOND', 'DECOY_EVALUE_PEPTIDE_QVALUE'... [-Wswitch]
switch (score_type) {
^
/Users/nobleadmin/proj/crux/trunk/src/model/MatchCollection.cpp:1780:13: warning: 15 enumeration values not handled in switch: 'XCORR_FIRST', 'XCORR_SECOND', 'DECOY_EVALUE_QVALUE'... [-Wswitch]
switch (score_type) {
^
/Users/nobleadmin/proj/crux/trunk/src/io/PMCDelimitedFileWriter.cpp:504:17: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
if (command = PSM_CONVERT_COMMAND) {
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/Users/nobleadmin/proj/crux/trunk/src/io/PMCDelimitedFileWriter.cpp:504:17: note: place parentheses around the assignment to silence this warning
if (command = PSM_CONVERT_COMMAND) {
^
( )
/Users/nobleadmin/proj/crux/trunk/src/io/PMCDelimitedFileWriter.cpp:504:17: note: use '==' to turn this assignment into an equality comparison
if (command = PSM_CONVERT_COMMAND) {